Nope, AxCrypt does not even contain the string “aep”, so there’s no way AxCrypt could have done that in the first place.
However, your sample file name “File Name.pdf-aep.axx” tells a different story.
This looks like a PDF file that was encrypted with “Advanced Encryption Package“, causing it to be named “File Name.pdf.aep”, and subsequently it has been encrypted once again, now with AxCrypt, causing it to be named “File Name.pdf-aep.axx”.
So, when you decrypt the file, it’ll once again become “File Name.pdf.aep”, i.e. successfully decrypted by AxCrypt. A PDF-file encrypted with “Advanced Encryption Package“.
The “File Name.pdf.aep” will of course not be recognized by AxCrypt or Acrobat, but presumably by “Advanced Encryption Package“.