If the encrypted file is opened with some other application(s) or it’s pending for re-encryption, then only we will a “file is open in another application” alert dialog.
So please check whether the file is opened with some other applications or opened application is running in a background process?.
Actually AxCrypt 2 uses a more robust method for the automatic re-encryption, which sometimes means you as the user have to tell AxCrypt to do it. You’ll see this by the “broom” icon becoming red. This indicates there’s something in need of “clean up”, i.e. re-encryption.
If the above does not help, please write a mail to firstname.lastname@example.org with the detailed information about the issue.