You need to understand what patching and your log returns actually mean before basing your post and assumptions on baseless accusations.

Just because one file is or is not patched here will not be the cause of a popup, especially when your log returns prove that the app is already patched.

Some files are left in intentionally for backwards compatibility so that they are covered in older versions; however, that does not mean they still need to be patched in latter versions.

Additionally, where the log returns "File already patched by GenP" and clearly shows "Patched", that means the file has already been patched and therefore does not get overwritten again.

If you simply click Search and Patch multiple times, nothing will happen after the first run as it only patches once.

To get the files back to their original state, you need to Restore first and then Patch again.

Still have issues after restoring the app and patching again, then simply do a clean uninstall of the specific app and remove any leftover app folder remnants, then simply reinstall and patch as clean again.

A basic understanding of how things work, which can be achieved by following the provided guides instead of relying on assumptions, would be helpful.

As for the unlicensed popup, that can happen to anybody at any time and is not just attributed to one single reason, especially when you do not provide your full log.

Alongside Adobe's multiple methods for triggering it, yours can easily be caused by a plethora of reasons on your own side and have nothing to do with GenP.

As for the popup itself, it is already well covered in the troubleshooting section; you just need to follow it like most others do.