Hello Danny,
AxCrypt will keep track on the opened encrypted files, to update and re-encrypt the same. If we opened the file and updated the contents, then AxCrypt will re-encrypt the updated file.
We have to close all the instance of the encrypted file(s) opened application.
For example: You opened an encrypted document and updating the document. At the same time, If you have opened another document in the same application, or even if just the application is running without an opened document, AxCrypt can’t be sure enough to actually do the re-encryption.
So we have to close all the opened application instances. If you closed all the instances, then you will not get any warning dialogs.
still your are facing any issue, you can feel free to contact our support via support@axcrypt.net .