The UserMerge extension currently does merge references of the fields fa_user and fa_user_text. However, it does not consider the field fa_deleted_user, which contains the user ID of the user, who deleted the file.
If there has been a file, which the user deleted using his old user account, then after the merge, the reference in fa_deleted_user will be broken, because it still points to the old user ID. It however should point to the new one.
To fix this, the field fa_deleted_user should still be added to the array of fields in UserMerge.php, function mergeDatabaseTables(), so that it gets updated as well!