Ultimately, there's no way to make any real sense out of the conflict between the narrative logic of events happening in a certain order and the realistic ramifications of time travel where causality goes out the window. It should
be possible, given the ease of time travel in the series, to go back to before anyone died and find them still alive. It should be possible to go back into the past of a now-extinct race and interact with them while they did exist. So the idea of any character or race being "dead now" from the perspective of a time traveler like the Doctor is nonsense. What constitutes "now" when you can be in 396,003 CE one day and 8 billion BCE the next?
But the narrative requires that events usually proceed in a certain order, that characters who die are still mourned as having been lost, that recurring friends or foes usually experience events in the same order the Doctor does, etc. So throughout its history, the show has always fudged the temporal logic. Usually it's just ignored the question altogether; otherwise it's made up arbitrary Laws of Time to explain why the Doctor can't just go back and save Adric or visit the young Brigadier or whatever, or concocted poorly-explained handwaves like "time locks" to justify the frankly rather nonsensical narrative conceit that a race that can exist throughout all of history is somehow "extinct" at any given point in the Doctor's subjective present no matter how far back or forward he travels.
So worrying or debating about how it can make sense is a futile effort. It doesn't make sense. It can't make sense. It's sloppy and self-contradictory and ridiculous. It's all just a bunch of arbitrary fudges that the writers came up with to simplify the storytelling logic. But in the case of Doctor Who
, that's acceptable, because it's all just a flamboyant, fanciful tall tale.