I've had this a few times now.. I had 0.9.3 installed, and upgraded to 0.9.5. I had a site installed using webapp-config, however once 0.9.3 was removed, and 0.9.5 was merged, (it was an upgrade, not slotted), my site had been removed.
Same here with error messages (see log)
Created attachment 88907 [details] Emerge log for trac-0.9.5
*** This bug has been marked as a duplicate of 136959 ***