This is happening to me and it's not permissions. Will save a file have worked on for days and I get a message file doesn't exist. This will happen in a sessions that I already saved the file a few times. Have to use save as. Then I see file 0.skp, 1.skp, .... Eventually saves. Sometime I keep trying and it works. Thought it was only imported files but now happeneng to some of my old files. Then thought it was because I was saving while rendering but that was it either.