Sounds odd, since I have seen the error but not in such a severe context. I would try to run part cleanup for a start. If at first it fails start a new session and open an empty file, then add you affected part to that as and assembly and run part cleanup on all loaded parts as a way around getting it to work.
By all means save a copy of the file if you can as the system may be set up in such a way that saving the file regenerates the faceted representations. If they are at the root of your difficulty then either saving or even manually deleting them can't do too much harm.
Lastly where you're certain that an affected file actually contains geometry as opposed to being as assembly then you might try to wind the model back to the first feature and regenerate the model all the way to the last.
All these things are about refreshing the file contents and ensuring that its contents are as they should be. The error behaviour sounds as if all is not quite right with the state in which it was last saved. Once again if assemblies are involved don't open all components by default. Rather you should open files one at a time to pin down the source of the problems.
