I would recommend reformatting to a linux fs if you possibly can. As mentioned, FAT has relatively low file size limits and might not handle permissions and ownership quite right. More importantly, FAT doesn’t track modification times on files as precisely as, say ext3 (FAT is only precise to within a 2 second window). This leads to particularly nasty behavior with rsync as it will sometimes decide that the original files is newer or older than the backup file by enough that it needs to re-copy the data or at least re-check the hashes. All in all, it makes for very poor performance on backups. If you must stick with FAT, look into rsync’s –size-only and –modify-window flags as workarounds.
