Uploading a gedcom file does not overright an existing tree, it creates a new one. You need to manually delete any old trees that you no longer need using the My Accounts page.
Note: If you have shared the tree, then the "Remove" option only removes your link to the tree and may not actually delete the tree and access to it for those you have shared it may remain. In that case you should use the "Send feedback" link to contact the F.E. administrator to ask for help.
