These are the top solutions for Desktop Hardware and Support:
Yes. Exclude each from the other's backup.
Make sure to exclude your external Time Machine volume from Retrospect lest it continuously try to back up that data. Likewise, don't have your Retrospect backup archive going onto an attached volume that Time Machine sees and wants to back up.
If you did not back up your keys, or if there is a problem with your back up, your Data Recovery Agent (DRA) can still recover your files. Submit a HelpSU request for assistance. If you have permitted other users to share your encrypted files, those users can recover your data as well.