I am curious, when one files an amended complaint, the complaint replaces the original one, correct? (i.e. one doesn't really Amend a complaint, they replace it with an amended one)

If this is the case, when one is directed by the court to only amend specific counts of the original complaint, what's the actual process for doing this? Do I modify the original complaint and ONLY update the counts they gave me permission to amend and resubmit the document in full as the "Amended Complaint" or do I file an "Amended Complaint" that only addresses the counts they directed to amend?

I want to make sure I don't shoot myself in the foot here by filing an amended complaint that omits previously supported counts.