Resolve migration issues: 2 identical copies of System photos (some photos aren't viewable on my iPad Pro though)

Ericnotes,

when you are viewing a library in Photos and the "Photos > Preferences > General: Use as system photo library" is dimmed and inactive, this library is the the system photo library. You can only enable "Use as System Photo Library" if it is not the System Photo Library. Only the items from the system Photo Library can sync with iCloud Photos to your other devices.

I don't use Adobe software, so I cannot tell you what the problem with Adobe Rush is. But in Photos 5 on Catalina it is nearly impossible to access the photos and videos in your Photos Library using the Finder, if that is what you are trying, because Photos 5 is renaming all original image files ( How Photos 5.0 on Catalina Manages original Files and Filenames). You are seeing the original filenames in Photos, but on the disk the images are having cryptic names. To edit an image with an external editor select the image in Photos and use the command "Image > Edit with" and select the editor you want. Or, if the application provides an editing extension, call this extension.

Another problem is, that not all image formats and video formats are supported any longer, that have been compatible in older system versions. Photos may have problems to process older items in the Photos Library. There is no list for Photos for Mac which older formats might be problematic. I am looking at the list for iMovie, when I am looking for older formats that need converting: About incompatible media in iMovie for macOS - Apple Support