Hi Shauna,
I just came across this unanswered question while doing a cleanup of the community. This one is a bit hard to decipher, but I do think you''ll end up with duplicate info if you make a lot of adjustments to the blueprint, especially depending how the content got into the target course. Syncing the blueprint, to my knowledge, is not a "replace everything in the course with only this stuff" but more like a "if this stuff doesn't exist or exists with outdated content, put the new stuff in". If this occurs again, I'd honestly recommend resetting the target course then resyncing it to the blueprint (assuming no student work had been done yet).
I hope this helps a bit, even though it's a very delayed response.
-Chris