Hello Vernon Stewart & Oshine,
AxCrypt is really detecting the files and secure your files in OneDrive.
If the file in fact is located in a folder designated as “Secured”, it will soon be re-encrypted again since those folders are monitored for unencrypted files and will encrypt them when you sign out, or click the “Broom” clean up icon.
After synchronizing your OneDrive files to your local, just encrypt those with the AxCrypt app. Once again sync your local with OneDrive.
Still, you are asking any issues, please provide more information about the issue and write a mail to email@example.com.