Call me stupid but I always have the same problem so I have got in the habit of backing up my config on the IDS and downloading the new .img file for the upgrades. I have had that happen to me way to many times.. It wont happen if you use the .img file though.. I promise you that ;)
Note: I said i backed up my IDS config because if you use the .img file you lose the config on the IDS as well.. Just an FYI.