A bad part.cfg wipes persistent.sfs and no parts at all are found.

[Galane]

Though this deals with additions to the base game, it's very bad behavior by KSP.

Some errors in part.cfg files will cause the game to delete everything from persistent.sfs except for flags and it'll pop up a window for every ship with a list of all the parts, stock and otherwise, claiming none can be found.

KSP should just ignore any malformed part.cfg files and ideally should pop up a window saying which ones it's ignoring and why.

I can provide an example of a part.cfg it won't load, and changes that make KSP nuke persistent.sfs.