That only adds to the puzzle. lol
I don't really think the thumbs are saved in our save files, 'cause if they were, there would never be this glitch, unless GT5 is a serious bad programmed software (and we know how buggy it is, not only regarding thumbnails, but a lot of other stuff). They have to be saved somewhere though, maybe the gamedata, or maybe they are indeed saved on our files. Nevertheless, whichever they are saved to, they shouldn't go missing or get wrong data from time to time when the triggers for this glitch, well...trigger it. All we can know for sure is that PD knew since the beginning the thumbnails had this glitch, as the restore function came with the disc version of the game. The only difference now is that they added a "restore to all cars" feature, but the "core" feature was present all along, since day one. It was annoying to do it one by one though. I guess we'll never really know everything about this bug, powerdrome.
Sometimes, when I send gifts to friends, I delete my save and replace it, so everything that I sent is there again. Several times, I went to my garage and all thumbnails were alright. That's what leads me to think they're not saved in the saved game data, 'cause, if I restore my original save after sending gifts or whatever other operations I want or need to do, the thumbnails are fine, but if I loaded an old save to do some operations (or if one creates a "new game save", it's the same as loading a different file than your original), and then replace with my original save, then the thumbnails get glitched. So, how come they get glitched sometimes, and not at other times ? This is why I think they're not saved in our files, but it's just a guess though.
My save file is currently at 2MBs, and I only have 200 cars I think. So, with 400 cars, assuming it's 1MB per 100 cars (in my case at least), my file will be 4MBs. You have 1.111 cars, so a save file of 4.3MBs... wow, you should consider yourself lucky, really! lol! xD