The crew transfer feature will certainly alter the crew numbers, but that is intentional. You get a summary screen telling you what's going on though. The feature doesn't run mid-patrol though.
But this is not related to the OP's question, which is a problem that I've seen raised numerous times since the game was released. It's simply a result of the flaky SH3 save system.
The OP should try to load the "in base after mission" save point (ie the mission before the one he wants to resume).
FYI here's a thread on the same issue first started back in July 2005!
http://www.subsim.com/radioroom/show...w+missing+save
There's other similar threads - the common theme is that the user has died, then attempted to reload the "in base before mission" save point. Crew gone.