Just a quick check. I’m thinking I may replace my existing non-encrypted B2 duplicacy storage with an encrypted one. I understand that I could initialize a new remote storage, and then use duplicacy to copy the old storage to the new. Will that be performed on B2’s end, or will duplicacy need to download all chunks and re-upload them? Thanks!
IMO 
doesn’t do anything server-side directly. But in your case it is even simpler, as you change encryption the chunks uploaded will be different, so everything will go through client-side.
Understood.
So maybe best practice / most cost effective strategy is to initialize a new encrypted storage and begin backing up the repository to it…leaving the old unencrypted storage in place and letting it prune and be phased out eventually?
I don’t know B2 cost structure, you need to run the numbers. Keep in mind that with two separate storages you will have no deduplication across, so there is a good chance that your storage will go up by up to 2x (if it is mostly static) or maybe not much at all if your revisions are small and you just have a lot of them. Whether or not running dual storages like that is acceptable for you, only you can answer 