@The Mighty Monkey of Mim The augment virus doesn't work like you think it does, as it has no effect on a Klingon's internal physiology. A Klingon affected by the virus would still have Klingon anatomical characteristics such as multiple lungs and stomachs, one less rib than humans, and a larger heart, all of which would be easily detectable to even a cursory scan, let alone the deep scan Tyler undergoes after coming back from Pahvo.
You're thinking of that
specific virus from the 2150s, which wasn't a deliberate creation of the Klingons; it was an
accident that arose out of a
larger program of research and experimentation in which they were trying to create Klingon Augments:
"Affliction" (ENT)...
PHLOX: Unless I'm mistaken, this virus is a mutated form of the Levodian flu.
ANTAAK: It's immune to whatever anti-viral we've tried.
PHLOX: We should contact the IME. They may have seen this mutation before. I'm certain they'll be willing to share their database with us. I know of a few indirect channels. No one would have to know.
ANTAAK: There's no reason to contact them. We've acquired their entire database.
PHLOX: You stole it.
ANTAAK: Medical research isn't a priority for the High Council. I am forced to obtain information however I can.
PHLOX: That doesn't sound very honorable.
ANTAAK: Given the choice between honor and saving lives, I choose the latter.
PHLOX: Perhaps you should ask your superiors to steal a genome sequencer? We're not going to be able to map the virus without the proper technology. This man's been infected.
K'VAGH: Very observant.
PHLOX: We're being exposed!
ANTAAK: This patient is at stage one. The virus doesn't become contagious until stage three.
PHLOX: When I asked you to bring me a subject for dissection, I assumed he'd already be dead.
[...]
PHLOX: I've seen these sequences before. Six months ago, to be precise. This is Augment DNA! How did modified human genes find their way into this virus?
K'VAGH: Is that really such a surprise, Doctor? It only took two human Augments to commandeer a Bird-of-Prey and murder its entire crew. The Empire could not allow an inferior species to gain an advantage on us. Imagine, every Starfleet vessel manned with genetically engineered humans!
PHLOX: Earth banned genetic engineering decades ago! The Augments who attacked you were relics of another era!
K'VAGH: The Vulcans told that to the High Council. They weren't very persuasive. We were simply responding to a threat.
PHLOX: You were trying to create Klingon Augments. But Soong's experiments were all killed. Where did you get the genetic material?
ANTAAK: Several embryos were found in the wreckage of the Bird-of-Prey. We used them to re-sequence a number of test subjects. There were some unanticipated side effects.
PHLOX: Their cranial ridges started to dissolve. Augment DNA was more aggressive than you realized.
ANTAAK: For a time, it appeared we were quite successful. Our Augments might have looked human, but they were Klingon. Stronger, more intelligent. Then, their neural pathways started to degrade. They died in agony. One of the test subjects was suffering from the Levodian flu. The Augment genes modified the virus.
PHLOX: It became airborne.
[...]
ANTAAK: They wouldn't destroy us if they knew we had created Klingon Augments.
K'VAGH: The experiment failed!
ANTAAK: It succeeded for a brief period. If Phlox and I can find a way to stabilize the human DNA prior to the onset of stage three, our Augments would survive. If we're successful, you could use them as leverage, force the High Council to give us more time to find a cure.
PHLOX: You don't seriously expect me to help you create Klingon Augments?!
"Divergence" (ENT)...
PHLOX: You want me to create Klingon Augments. Living weapons. I won't do it.
ANTAAK: No, no. I've been reviewing your work. It's brilliant! You have discovered a weakness in the virus causing the plague. If we interrupt the transcription sequence here...
PHLOX: Yes. Yes. That would stop the genetic effects of the virus in stage one. There'd be changes of appearance, some minor neural reordering, but no development of stage two characteristics. No enhanced strength or speed or endurance. But then General K'Vagh would not get his Augments. He would never allow it.
ANTAAK: What if we don't tell him?
[...]
PHLOX: As a physician in the Imperial Fleet, you've served in the military.
ANTAAK: Not as well as I should have. I did not screen my subjects properly. This plague, all its victims, it's my fault. My failure is the reason you're here.
[...]
K'VAGH: Report.
ANTAAK: Doctor Phlox has made excellent progress.
K'VAGH: Details.
PHLOX: I've identified the RNA sequences that code...
K'VAGH: Details I can pass on to my superiors.
PHLOX: I know where to look for the switch that will turn off the virus.
[...]
K'VAGH: The Denobulan is close to perfecting the Augments' genome.
KRELL: The Council has shut down your project.
K'VAGH: If you sterilize this colony, then all our research will be lost.
KRELL: The fleet will reach you in three days. If you're successful by the time we enter orbit, Qu'Vat will be spared.
[...]
PHLOX: General, I know the Klingon fleet is on its way, and I understand what this project cost you, personally. Antaak told me about your son.
K'VAGH: He died in combat for the Empire.
PHLOX: At least he was spared the final stage of this disease. May I ask how he was infected?
K'VAGH: Command chose his unit for the Augment experiment when we had exhausted our supply of prisoners. My son was a warrior. He asked for no special treatment, and I gave him none.
[...]
PHLOX: One of these four strains has the genetic trigger that can neutralize the virus before it advances to its lethal stage.
K'VAGH: Which one?
PHLOX: I don't know yet. That's why I have to check each of them.
K'VAGH: How long will it take?
PHLOX: A week. Your fleet can quarantine this world while I complete my tests. Sterilization is not necessary.
K'VAGH: Fleet Admiral Krell will not extend his deadline.
PHLOX: The only possible way to get results on Krell's schedule is to infect four healthy Klingons!
K'VAGH: You have four right here!
PHLOX: Only one of these strains will work. The other three will be lethal. Ethically, it's unthinkable.
K'VAGH: The ethics, Doctor, are simple. Three lives to save millions.
[...]
PHLOX: I need a little more time to cure this plague.
K'VAGH: Cure!? You were supposed to perfect the Augment genome!
PHLOX: I lied.
[...]
PHLOX: Why did you think you'd succeed in perfecting Augments, when Doctor Soong failed?
K'VAGH: Soong's mistake was that he made too few of them.
PHLOX: The Earth once had thousands. They became tyrannical and started a war.
K'VAGH: Klingons have discipline.
PHLOX: Augments don't. Their increased aggression is matched by their decreased inhibitions. You'd lose control of them, just as humans did.
[...]
ARCHER: Captain's Starlog, supplemental...Admiral Krell has convinced the High Council to call off their sterilization program. They've promised to distribute Phlox's cure throughout the Empire.
PHLOX: There's no trace of the virus in your bloodstream.
ANTAAK: My targ won't even recognize me.
PHLOX: In the future, it may be possible to reverse the cosmetic effects.
ANTAAK: I suppose this is what I deserve. Millions of my people will have to live with this disfigurement. It'll be passed on to our children. Life won't be easy for us.
PHLOX: You did your best to correct your mistakes. That's all we can ask of ourselves.
ANTAAK: I doubt my superiors will allow me to remain in my position. I'll need to find a new specialty. Perhaps cranial reconstruction.
PHLOX: I have a feeling that's about to become very popular.
Phlox helped them devise an anti-virus that would arrest the progression of the plague, which was then "promised" to be distributed throughout the Empire. But all that research was ultimately
preserved. Over the next hundred years, even if the High Council had abandoned it, Mókai's House of Spies could well have drawn upon and utilized elements of it to their own devious purposes, seeking to perfect infiltrators who could pass among humans undetected (if not for those troublesome tribbles) instead of über-KlingKhans. Indeed, the very same ENT story suggested that similar tactics were effectively practiced in other contexts even then:
ANTAAK: I wouldn't expect you to remember, but we met briefly five years ago, at the IME conference on Tiburon.
PHLOX: I don't recall meeting a Klingon at that conference.
ANTAAK: I was disguised as a member of the Mazarite delegation. My people weren't invited.
His disguise there may well have been of a cruder nature (though obviously
not so crude as to be revealed before a conference full of doctors!) than what we're discussing in this case, but that isn't the point. The point is we have examples of Klingons managing to "sneak in" and remain undiscovered (at least for a while) which both pre-date and post-date DSC. It's something they do, and have some skill at. Arne Darvin wasn't the first, and he probably wasn't the last.
Oh, and let's not forget the fact that Section 31 was tied up in all this as well, having made an arrangement with the Klingons to deliver Phlox in the first place...
ARCHER: Where's my doctor?
HARRIS: He's safe, on a mission of great importance to Starfleet.
ARCHER: Phlox was kidnapped. Starfleet would never authorize that.
HARRIS: Re-read the Charter, Article 14, Section 31. There are a few lines that make allowances for bending the rules during times of extraordinary threat.
ARCHER: What threat?
HARRIS: Take your pick. Earth's got a lot of enemies.
ARCHER: Klingons attacked my ship. Is that what we're talking about?
HARRIS: What I want to talk about is Lieutenant Reed. He's done good work for us over the years. Don't be too hard on him. He was just following my orders.
ARCHER: You put him in an impossible position.
HARRIS: I can understand why you would feel that way, but this is bigger than one captain and one ship.
ARCHER: You're going to have to do better than that.
HARRIS: All I can tell you is that if you interfere before Phlox completes his assignment, the repercussions will affect entire worlds.
[...]
REED: I thought it was done. This is the first time that Harris has contacted me since I've served on Enterprise
. He told me about the plague. He said they needed Phlox to help the Klingons find a cure. I was supposed to just slow us down.
ARCHER: Did Harris tell you about this? I had T'Pol take a closer look at our prisoner's medical scans.
REED: That's human DNA.
ARCHER: I'm guessing the plague is a side effect of a military experiment that went wrong.
REED: I didn't know.
ARCHER: Harris claims he's doing this because Starfleet needs a stable Klingon Empire.
REED: Do you believe him?
ARCHER: I don't trust him. If the Klingons needed our help, there are easier ways to get it.
[...]
HARRIS: I called to thank you. Everything went according to our projections. The Empire's been stabilized. I doubt very much they'll be experimenting with Augments anytime soon.
And of course, we all know that Section 31's machinations always go just as planned and never, ever backfire or have consequences down the line, right? (Ooooh, here's a spontaneous out-of-left-field thought for y'all: could the twist be that, rather than Tyler being Voq in disguise,
Voq was Tyler in disguise? A human Section 31 agent who was passing as an albino Klingon?

)
As far as this "mind sifter" idea goes, DS9 establishes that while the transference of one's personality and menories into a different body IS possible, it creates neurological anomalies that are detectable and would immediately raiuse red flags.
As I've
said before, that is not accurate. Any anomalies could
only be detected by
first identifying the
specific method of transfer and
knowing what to look for:
SISKO: It doesn't make sense. She's been doing everything she can to convince us that Vantika is alive. If Vantika's controlling her, why would he call attention to himself?
DAX: We're not suggesting he's controlling her.
BASHIR: This is all theoretical, but to extend the logic, there's no reason to believe she'd even be aware of his presence.
DAX: Like a stowaway on a ship. The pilot's at the helm, but someone else is along for the ride.
SISKO: Would an examination of Kajada confirm any of this?
BASHIR: We don't know what we're looking for yet. We still have to identify a method of transfer first.
[...]
BASHIR: Well, I haven't noticed any indication of suicidal behavior, but then, who knows what the effect of sharing one's brain might be?
SISKO: I'd still like some confirmation of that.
BASHIR: I'll have to tend to her injuries before I conduct any brain scan, but until we find the transfer method Vantika used, I'm not even sure what to look for.
And keep in mind that this episode
began with Bashir bragging (and not entirely in vain, either) of how he had a singular gift for examining details and finding things any other doctor might easily have missed...
KIRA: I've never seen anything like that.
BASHIR: The woman?
KIRA: She was dead. The tricorder clearly showed...
BASHIR: Ah yes, well, tricorders...very accurate with live people, not so accurate with dead ones. We learn that first year medical school.
KIRA: Well, I was very impressed, Doctor.
BASHIR: And well you should have been. I impressed myself on that one, actually. I can't imagine what other doctor would even consider examining the scapular nodes for parasitic infection. I just seem to have a talent, I suppose. A vision that sees past the obvious, 'round the mundane, right to the target. Fate has granted me a gift, Major. A gift to be a healer.
(Hmmm...come to think of it, Bashir was
both an Augment
and a Section 31 agent, wasn't he? Is Tyler a time-traveling-mirror-universe-recast-visually-rebooted Bashir? My mind hurts now, I'm ready to have it emptied...

)
I don't know where Voq has gone, but his disappearance doed not automatically mean he was turned into Lt. Tyler.
No, it certainly doesn't
automatically mean that by itself. But it gives yet another reason to ask questions. And if both characters are played by the same actor, and they've gone to some lengths to conceal this, and other elements of Tyler's story don't ring true...that all needs to be taken together. Now, it could still all be misdirection. But I don't understand your staunch denial of the mere
possibility.
-
MMoM
(if I dare sign my name to that)