I wanted to have a backup of my Dropbox on my NAS, so I used Synology's CloudSync service to back up to an encrypted folder. Unfortunately Synology's encryption actually encrypts each file individually, which Dropbox happily syncs to all of the computers that use that Dropbox, making all of those files unusable!
In the end, I had to write a script that detected which files were encrypted (files start with `__CLOUDSYNC_ENC__`), then use a WINDOWS ONLY decryption utility provided by Synology to decrypt and finally get back to a clean state. Then I wrote another script to move the decrypted files back into the proper path in Dropbox while correcting the newly decrypted files with the original metadata (creation date) from the encrypted bad files. What a pain!!
I'm still not sure of a good way to achieve my original goal of backing up Dropbox while still protecting my data with encryption. Let me know if anyone has a solution!