CiviCRM Contact Information Merging and Overriding Unrelated Users/Donors
Oh dear, yes that sounds like things are in a mess. Some suggestions


It sounds like you need to review the Dedupe Rules that are set up and in use. That should include checking that the 'threshold' has been set correctly
You should check if logging is turned on (civicrm/admin/setting/misc?reset=1) and hope that it is as that should let you use the Change Log tab to try and identify and restore changes
if you have access to the db and have access to some sql skills then you may be able to repair some of the problems