If there are more then so many I think 500 duplicates or assumed duplicates, it will create a fail. You should be able to split your gedcom into smaller chunks. Work on any issues on that smaller section. Then continue. You can have an intentional merge "anchor" person to merge on upload just as a place marker.
Trust me!! (infamous last words) you do not want to upload everything all at once. Even 1000 if you go thru and hand merge everyone. Wikitree is not the same critter as rootsweb, ancestry, or even familysearch.
I would suggest that you see if any one in your gedcom is already listed. And build from there. Its not about how many gedcoms we upload, its about building one tree and having verifiable documentation.
You really do want to learn how Wikitree operates before you upload a bunch. Its really easier to hand list them with proper documentation, then it is to add everyone all at once and attempt to sort thru it later. This I learned the hard way. And I only uploaded 500 my first time.
I have 10,000 in my db, but I have only uploaded about 2000.