You can just upload a new GEDCOM to Ancestry. It wont overwrite the one that is there but will create a new tree alongside the old one. You will of course need to give it a different name to distinguish between the two.
Once you've uploaded it and you know it has worked correctly it is a good idea to remove the old one or else you will end up with a number of trees on Ancestry and will get confused as to which one is the more recent.
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