[[!comment format=mdwn username="http://joeyh.name/" ip="4.154.0.21" subject="comment 5" date="2013-07-30T18:39:58Z" content=""" Your transcript shows unannex without --fast having the problem, and uninit not having the problem. Which is just what I said. Although I had to spend 15 minutes reading and replicating your transcript to figure that out. This has been previously reported and discussed at [[Large_unannex_operations_result_in_stale_symlinks_and_data_loss]]. There does not seem to be a single entirely satesfactory solution. unannex --fast seems to be what you're looking for. """]]