You can upload another GEDCOM with the new folks in it, hopefully only duplicating those that link up. You're right, that new GEDCOM uploads will not replace previous ones, so you really want to limit the number of duplicates. If there are too many duplicates in a new GEDCOM upload, the file will not process. You can upload several small files - some folks upload a family at a time, from 4-8 people. Others upload a generation at a time. I hope this helps.
~tami, WikiTree Cousin Connector