Server side copy comes into effect when you copy something in the same provider, so if you do
rclone copy acd:dir1 acd:dir2
that is an opportunity to use server side copy. Amazon cloud drive doesn't support server side copy anyway though, but other remotes do.
If you set up a crypted remote on your ACD lets say pointing at
I'd use the web interface to move all the current content into a subdirectory called
unencrypted. Then you would do
rclone copy acd:unencrypted secretacd:
rclone will download stuff and upload it again, encrypting on the fly.
That would only work with crypt. If you wanted to use EncFS you'd need to download it all locally I think.