I'm having this same issue. C9 seems to have lost track of the save status. The file tabbed icon continues to spin after loading a file. I'll make changes save, continue on another tab come back to the tab and it will say "Contents of file have changed on disk, do you want to reload?" I'm never sure which file it's going to "bring back". I've tried restarting, closing all tabs, etc, but nothing seems to work. Any suggestions?