Duplicate object found in source - ignoring

[ncw (Nick Craig-Wood)]

when running the sync command, it shows me similarly named directories and an encrypted string as duplicated. i suppose this means that each one is duped, not that rclone is mistaking them for being dupes?

The detection of a dupe in sync is just that the names are identical.

when I run rclone dedupe remote1_crypt:

i get the error: Failed to dedupe: Encrypted drive remote1_crypt: can’t merge directories

That is a bug - it means the crypt remote isn’t passing on the merge request to the underlying remote properly.
I made an issue about that https://github.com/ncw/rclone/issues/2233

However you can dedupe the underlying remote and it should get rid of that duplicated directory for you. Don’t rename any of the duplicates though as they will become invisible in the crypted remote.