Is prevented best by sticking to the recomemnded naming schema.
If you have particularly hard to match items (i.e. because they are ambiguously titled or there were several titles by the same name in a year), then use the database ID matching hints in the folder names.
Plus the side note I mentioned above about multiple pairs of square brackets.
Can be prevented with a bit of preparation and a backup. See my post from earlier today: PSA: Script to back up and restore Plex app data on a Windows system - #30 by OttoKerner
