Apple no longer supports the legacy iTunes 12.6 w/ios apps.
If trying to update to iOS 13 and having issues, or, updating 13 OTA and then having issues w/itunes 12.6, it is because they are not compatible. Apple will not be giving us another update to iTunes 12.6 for iOS 13 compatibility, they are trying to move people to the in-device app store.
Dilemma:
Not sure what to do, I want to update to iOS 13, but, my options are: update OTA and no longer use iTunes, which means I have to enable iCloud backup, which I don't want, I prefer backup on my Mac and my Mac's backup. OR update iTunes and no longer be able to swap old iOS apps that still work but are unavailable for my iPad Mini (1st gen.) running iOS 9.
I guess my last option would be to make another system on a spare drive with iTunes 12.6 to use just for the iPad Mini, but, there are other reasons for not wanting to update, and, I really don't have the time to build that right now. Ugh.
Does the newer version of iTunes not back up your phone when syncing? The apps issue isn't unimportant, but if iTunes still backs up all is not lost.