I also have Autosave disabled because it can save “errors” or stages in the workflow that you do not want and it is demanding on system resources that may be needed elsewhere while I edit.
I have a CTRL-S habit and I keep a backup copy of the project that I regularly save to (on major chnges or every half hour – whichever comes first).
The dissapearing transitions issue from the OP is a mystery and I can not even think of a way to do it if I wanted to.
(Maybe some render files got deleted).