Just to emphasize, once an uploaded GEDCOM *is* processed, then uploading a second version (with the same people) will require merging all the duplicates it creates. It will also not get rid of any people or relationships that were deleted. In this case Eowyn has indicated your original GEDCOM had not been processed yet.
Like most people, I keep my personal files in GEDCOM-compatible software but make all my Wikitree profiles manually, and always advocate others to do the same. While it sounds like a lot of work, it is actually about equal to matching, merging, and cleaning up the merged profiles. It also gives you an extra opportunity to look over the information to spot any errors or omissions that might have been made when you recorded the data.