Ok, I found why it's crashing, it happens when the number of sprites record in the game is larger than in the sprite file. That would be trivial to fix.
Idk why the backup problem happens. Nothing changed there in a pretty long time, so the error itself may be legitimate (maybe something prevents AGS to access a file? Question is which file - sprite file itself or its backup).
But looking at the program logic there, it's definitely incorrect because AGS refuses to continue saving sprites if it failed to make backup, which is silly imho. I'll try to change that to something more reliable.