Awesome, I think it's all sorted out now with your suggestion. I mounted the ISO and fired up AnyDVD which showed the SP detected. I ripped it to a folder and it seems to have stripped out the fake files. The folder came out the right size and has no duplicates. It plays fine in VLC as I can see the menu and select the episodes and all the extras. But with that being said, also the messed up ISO plays fine in VLC anyway.
In the DVD folder that I ripped with AnyDVD I see the main VTS is now VTS_10 and I think on the original disc it was VTS_03 because my other DVDs from the set have it at VTS_03. However I can't check the damaged disc. Oh well, this is as good as it's gonna get. At least my backup wasn't totally lost even though it might not be a 1:1 perfect copy, it's still fine. BTW I never got any warnings from AnyDVD like you said simply because I never actually used the AnyDVD ripper. I just fire up AnyDVD in the background and then use imgburn most of the time or other ISO rippers. I never even look at AnyDVD, not even changing any settings. I just thought it always works in the background so that's my mistake.
Yeah now I'm in the process of backing up the rest of the discs all over again the right way this time. Plus also checking through my other backups because I wonder if I messed up with other ones too. But now I learned to rip to folders! That's what I'll be doing from now on. I never even knew about this difference between ISO's and folders. I'm just gonna keep my backups in the folder format.