Is this happening only in this particular session? Or does it happen in any other sessions as well?
I once had something similar occur, only to realize that my Shift key was stuck (or was it Alt? I forget... it was a long time ago), so it was applying my edits to all tracks. I thought I was in the twilight zone there for about 30 seconds before it dawned on me what was going on.
Since you mention this was once a HD session... by any chance did this session utilize VCA groups? That's an HD feature only, and separate from regular mix/edit groups, and since they don't exist for LE or M-Powered, I have no idea how they transfer over. Hmm... that's an interesting question in itself.