First, are you sure you installed the 3DO's official 1.2 patch first? The files which our patch refused to update are the ones which were amended with the 1.2 patch. If you didn't run the 1.2 patch then those files could not be updated by the 1.3 patch.If this is the case (and I suspect it is) then the recovery is quite simple. Unless you told it not to, our patch made a copy of the original files which it did update -- data\WORLDS.REZ, data\LOCALART.REZ, and data\RUDE.REZ. You can find them in a new folder called PatchWise.bak\data in your MM9 installation folder.
Copy those original files back to the 'data' folder in your MM9 installation folder, get the 1.2 patch, and run it. Now you can install the 1.3a patch.
You can get the 1.2 patch from several places. The URLs are in that 'TELP13 User Guide.txt' file in your MM9 folder. It's a remarkably useful document.