Yes it does happen
I had a spell of my playlists having the same problem and I think its something to do with the rescan folder (nightly)
I have now changed the schedule to never and rescan manually and haven't had a problem since.
Remember you can export your playlists for safe keeping.

Edit: thanks Hakko for picking up the changed drive bit - its possible that Sindre is using drive ID (which changes) rather then path internally