So, the dice decided to have a laugh at me for mentioning that my PCs could theoretically lose their lead on Hadarak Fel. On the warp trip from the Battleground to Footfall, it put them another three weeks early.
Based on the sheer amount of time that they'd gone back, the fleet managed to arrive at Footfall with the Captain they picked up at Port Wander (about half the crew were serving aboard the Peregrine prior to the beginning of the game, and the other half came on with the Captain, who was being given her first command by her Dynasty), before they left to go get her in the first place.
I had them make Intelligence checks, and since I'm NPC-running the ship's Explorator, I had him argue for reason and logic and not screwing with the timeline. I also had him make contact with his earlier self through the data network set up in Footfall to let himself know what was going on and that they needed to leave. I also mentioned that the PCs who had been on the ship previously remembered their departure seemed kind of rushed.
I also mentioned to one of the players who has a character who's had friendly dealings with the Inquisition before (specifically as a member of an Inquisitor's retinue who was given leave to become the ship's Seneschal in exchange for an undisclosed something that even he wasn't able to find out the nature of) that there is a minor order devoted to dealing with wibbly-wobbly timey-wimey stuff, and trying to mess with things too much would probably get them all executed, or worse.
I also mentioned to them that the dockworkers had heard tales of the Warp spitting ships out at the wrong time, and most of them "knew a guy, who knows a guy, who knows a guy that it might have happened to", so no big issue with the fleet leaving, docking, then jumping there.
I think I'm going to fudge the rolls in the future, though. This is Warhammer 40k, not Doctor Who.