Each time you install a new build from JRiver, the transponder list files are replaced with our version. Therefore you should, 1. save a copy in a separate place, 2. better yet, forward a copy to me, so I can include it in the next build.
I believe the same program can be broadcast on different transponders (frequencies). After channel scanning is finished, you can run Manage Channels tool to hide duplicate channels. Do not delete them, hide them. This way when you rescan the hidden channels will remain hidden. If you delete a channel, and then rescan, it will come back.
Rescan option will rescan all frequencies. Channel scanning is not a task that you will perform often. If you really want to customize how you scan, the only way to do it is to edit the transponder xml file so you keep only the frequencies you want to scan. That seems to be unnecessarily complicated. If it is just one channel that you need to change, it might be easier to just manually edit that particular channel, assuming you can find the parameters for that channel by other means, such as Internet search.
All channels, including hidden channels, are saved in the library backup.
If you do not mind losing your previous customization of Theater View, I believe you can just do a Reset in Theater View settings. If you do need to keep other customization, you then will need to setup Guide manually. Someone might have posted some sort of instructions on it, but I do not remember.