I need this to be resolved quickly so if anyone has any information on how to solve this it would be much appreciated. Since PanoTour Pro does not allow you to replace a map file in the program without removing all it's hot spots, I opened the kpt file in Taco HTML Edit, and replaced the map file name and hit save. When I reopened in PanoTour Pro it screwed up many, many things. None of the hotspots lead to the correct pano. Some of the hotspots on the map are gone. One of the panos went missing but it looks like that data is no longer in the kpt file.
Here's one clue of something weird I noticed: A long string of text inside the kpt displayed japanese characters.
Please don't tell me to make backups because I usually do. I just didn't think changing one number inside a kpt file of an image filename would mess up everything.