Same issue here, but I've to add another serious consequence (I'm syncing a folder inside a TrueCrypt volume and when I rebooted that volume was not yet mounted when SyncApp started): the missing folder seems not to be detected as missing but instead it is just considered 'completely empty', so SyncApp started to delete all files on another machine running the client. I double checked that's this is not just an issue about an existing but empty mount point (since the parent directory is also missing), though this shouldn't happen with just an empty mount point either. I'm running Mac OS X 10.8.2 on both sides.
