I have been keeping an off-site backup clone using SuperDuper (as well as on-site clone and time machine). I have been using SuperDuper in "Smart Update" mode so that only changed files are backed up each time. I decided to look at the backup clone with Disk Warrior and found that even though Disk Warrior reports the original desktop has perhaps 2% "items out of order", the clone drive has about 40% "items out of order" in the directory. I am assuming this is due to the smart update changes to the clone.
Should I repair the clone with Disk Warrior (since there are so many "items out of order") or will that cause other problems and should I leave well enough alone?
Alternatively, should I occasionally do a complete erase and copy in SuperDuper so the file directory does not get so out of order?