In that case, if you still have the downloaded archives as backup, i'd do this: check the file extension of the mod archive, either .rpy or .rpyc (for this example, let's say the mod adds .rpy files), go into your root game dir, open a command window (cmd, shell, powershell depending on your OS) and delete with the 'search in subfolder' option these files:
s0*.rpyc
script1.rpyc
script4.rpyc
mirandaAcceptSex.rpyc
mirandaBJVisit.rpyc
victoriaYogaVisit.rpyc
willowRoute.rpyc
This will purge all double definitions, however keep in mind that the s0*.rpyc is a broad wildcard and MAY break your game with a 'label not found' error, probably while playing, if the mod does NOT modifies a random script file.
If that happens, here's the solution: in the error screen you'll se the traceback for either the call or jump instruction and it will tell you the file name s0__x.rpy, go back to the ORIGINAL archive and copy back in your game folder the s0__(x+1).rpyc file, reload and continue