WARNING - if you index files, BE CAREFUL with how you install new Dropbox + Mac OS [edited!]

Maybe these 5% were already updated before you could stop everything? You might try this:

  1. Disable scheduled/automatic sync and also sync on quit/deactivation. Alternatively disable all sync locations.
  2. Enable the hidden preference DisableFilesystemEvents

Now restore the backup again and update the paths. Did it work this time?