We are already explain, please read our previous reply in the below link.https://www.axcrypt.net/forums/topic/desktop-ini/#post-15595
You can encrypt a folder by using Secured Folders option. After that if you create a subfolder, it won’t re-encrypt the files of subfolder.
We can include the sub-folder by enabling the feature from the AxCrypt app menu File | Options | Include Subfolders. By default Include Subfolders will be disabled. So Sub-folders are not encrypted without enabling this feature.