All programs crash, and new programs (like this one) crash a lot.
Every minute or so FontForge looks around and sees if anything has changed since the last time it checked. If it finds a font that has had changes, it will save a small file in its private directory (~/.FontForge/autosave) which consists of all changed glyphs in the changed font.
When FontForge starts up it checks this directory, and if it finds anything there it attempts to apply those changes to the original font. So if FontForge crashes, or if your machine crashes, the next time you start FontForge it will figure out what you were doing and recover it as best it can.
When editing CID-keyed fonts there are a few potential gotchas: