Each GEDCOM you upload is a separate file. One uploaded GEDCOM file will not/cannot be combined with another uploaded GEDCOM file at WikiTree.
You can have multiple GEDCOM files in the system, so you don't risk losing the work you've done on your current file - unless you haven't accessed it for 60 days or more.
I would not recommend replacing your current GEDCOM. Just upload another (preferably smaller) file if you feel you are not making progress on your current file. You can always come back to your old GEDCOM (within 60 days, of course).
The GEDCOMpare process can take time to learn. But once you learn it, you will find future GEDCOMs become easier to work. Stick with it, and let us know if you run into problems.
edit: added link to GEDCOMpare