Hi Arnold, it sounds like there's a bit of a misunderstanding around trees and gedcoms. A gedcom is not your tree -- its a transfer file format that contains the basic information in your tree.
WikiTree has a two stage import process. The first stage, is called GedCompare. In that stage, one uploads their GedCom file to compare with what is already on WikiTree.
The second stage does the actual transferring of information into the public, shared tree here on WikiTree.
If you did not complete that second stage, then there is nothing to delete (actually there is, but no one else has access to it, and it will be automatically deleted after 30 days -- find the link to delete at the bottom of your compare page)
If you did complete that final import stage, then uploading a second, larger or more complete GedCom will obviously contain duplicates of the first one that will either have to be skipped or edited. There's no other way around that.