Yes, they seem are likely doubly encrypted. First with “Advanced Encryption Package”, and then with AxCrypt.
In the light of this, I don’t really understand your statement “What I still don’t understand is the double futile extension—the “aep.axx.” It makes it seem that the files with that extension are doubly encrypted“.
First you encrypt the file with “Advanded Encryption Package”. This tacks on the “.aep” extension to the original.
Then you encrypt the file with AxCrypt. This changes the “.aep” to “-aep”, then tacks on the “.axx” extension
So a file named “File.pdf-aep.axx” seems to be double encrypted because it is!