I want to move the contents of my S3 special remote. I've already kicked off the transfer with rclone sync s3:bucketfoo s3:bucketbar/annex to move the encrypted chunks to a new bucket under a new prefix. Once that finishes (in a few days), can I just run git annex enableremote [new params] or will I run into problems?

git annex enableremote bucket=bucketbar fileprefix=annex/works just fine.Thanks for sharing the answer you found, it helped me out as well.
To add on, modifying a special remote via
git annex enableremote myspecialremote autoenable=true && git annex syncalso propagates the updated configuration to reachable repositories. That said, you have to manually remove and re-enable remote to get the new configuration for each repo.