NoteBookUser I'm not sure if I understand correctly, but it seems that you have the inner working of the old Boxcryptor App in mind - the 3.x version on MacOS works significantly different.
Boxcryptor no longer has a physical folder that it creates and to which the encrypted files are stored. This was necessary with the old version, as Boxcryptor did not do the synchronization itself but left it to the sync app of the provider.
The new app is talking directly with the provider online. That means that every folder and file you see when browsing into the Boxcryptor location is not really existing on your system yet. It only gets downloaded when you open it or specifically request "Download Now" from the context menu. But even in that case, there is no singular or well defined folder in which the files get downloaded. Boxcryptor downloads the file and hands it over to Finder itself, which is then responsible to store it somewhere. But this is outside of the control of the app.
This also means that any workaround expecting a folder "below" the Boxcryptor location cannot work - there is no such folder. It also means that there is no necessity to re-encrypt or re-upload anything. If the Boxcryptor files have been synced to the cloud, you will have them displayed right in the Boxcryptor location and can work with them from there.
That being said, there is an easy way to simulate the inner working of the old Boxcryptor app if you want to do so: Install your cloud storage provider's sync app and add it to Boxcryptor as a local storage. Then, you have the intermediate folder that you were looking for in the form of the provider's sync folder.
Best regards,
Christian
