So we are assuming 2 time jumps then, the Diviner travelling back to when Chakotay was commanding the Protostar, and then the Protostar being thrown back to TNG Season 3, and lost until the kids found her again.
We are going with 2 jumps with available information (or at least I did).
First one was intentional (the Diviner's original 50 year jump to the past - before SF's First Contact with Solum), and the second (accidental) one which threw the Diviner/Drednok again over 17 years into the past WITH the Protostar (to before 2366).
If you recall, during the '17 years ago' sequence (just before the Diviner decided to make Gwyn), Drednok mentioned that there have been many failed attempts at finding the Protostar for 'years' (possibly more).
So, the Diviner/Drednok ended up roughly 70 years into their past... whereas the Protostar ended up roughly 20 odd years into its past.
I already presented a sequence of events before where I said the 'anomaly' Chakotay mentioned in his distress call was the one created by the Diviner's first temporal jump from around 2433.
Drednok then boards the ship, attacks the crew and Chakotay (also discovering Chakotay's command codes in the process) and the Diviner uploads his weapon into Protostar's systems. Chakotay and the crew (or just Chakotay), manage to take back control of the ship somehow, but something goes awry because the original anomaly is still there and something as a result of Chakotay's efforts to escape causes the animaly to throw both the Protostar and the REV-12 (assuming the REV-12 was built originally around 2433) into the past.
Chakotay then realizing the ship is in the past along with a weapon from the Diviner that could destroy Starfleet, manages to hide the ship inside Tars Lamora (where it would be surrounded by Chimerium and make it invisible to sensors). I guess he figured it was the best way to avoid damaging/altering the timeline and preserve Starfleet. Though, one would have thought in that case: why didn't Chakotay just initiate self-destruct in the past to prevent the ship from ever being a threat?
One possible explanation is that Chakotay didn't know about Diviner's weapon, and wanted to make use of the Protostar at a later date when sufficient time has passed... the self-destruct mechanism may have been damaged, or because the Proto-core presented a too big of a danger to the environment if the ship self-destructed... but then Chakotay could have simply Proto-Jumped away thousands of Ly's (out of the Diviner's grasp)... but the Proto Warp could have ended up damaged at the time, so the only viable thing would have been to hide the ship (with running not being an option) and allow the self-repair systems to repair critical damage before powering it down permanently.
Also, if you want to go further down the rabbit hole, the Borg also could have factored into Chakotay's decision. I mean, they were still perfectly fine in that time frame, and why would you want to risk them potentially assimilating the thing (plus, Tars Lamora's position in the galaxy would have also been near that TransWarp Hub VOY destroyed).
I somehow think they may have missed a few possible options/steps if my hypothesis is accurate... or because of his encounter with the anomaly, Chakotay realized the Protostar will play a bigger role at some point down the line and the ship had to be preserved, and that anything short of that could present a problem?
