Yeah, I personally suggest having a script run through the mod without the hotfix and then the mod with the hotfix and then automatically generating a file indicating which files are to be updated. This file can then be sent to clients and they can just overwrite the files rather than going through all files on a client's machine. Or, alternatively, you could just package an archive of only the update files and extract the archive and have it overwrite all existing files. (apologies for double post, I'm used to MyBB post merging)