If I understood this correctly, your library backup file contains the old smartlist rules, but in addition of the wrong base path also many of the filenames are now wrong in this backed up library. This problem is indeed difficult to fix with the Rename, Move, & Copy Files tool unless you can replicate exactly the same settings and rules that you used when you copied the files. If you can replicate them, you can load the library backup file and do the same copy process as before, but this time select the option to apply the changes only to the database. It should then be able to fix the filenames and paths only inside the database.
Another option is to export an MPL playlist of your current, correctly linked files, restore the library backup file of your old library, delete all files from the library (this will preserve the rule based smartists even though they will be temporarily emptied) and finally import the MPL playlist, which will just restore the files.