AxCrypt app will encrypt most of the file types like mp4, txt, pdf, jpg, etc. Also some file types AxCrypt will not encrypt due to security reasons.
It may be the pdf file is a hidden state. So check the file properties the pdf file is hidden state or not? If hidden the file means, Please remove the access, then to encrypt the files.
If you are receiving the warning dialog frequently, please click the Don’t show this again option. After that, you never see this kind of warning.
Still, if you are facing any issues, please write an email to firstname.lastname@example.org with some more information about the issue. If you can send a screenshot showing where the problem is, it often helps us understand.