For those of you who do not know how to import your GEDCOM file into your existing tree: you can do this by uploading your GEDCOM file to here using a different email address than is associated with your existing tree on Geni. After the import is complete make sure your profile name is set the same on both accounts and then you can enter your other email address into your existing profile (additional email) and it will ask you if you want to do a self merge, which will merge both accounts and trees. If it does not ask you to do a self merge, login to your other account and it will ask you if you want to merge trees.
Note: At this time, any one GEDCOM file cannot contain more than 50,000 people. However you could break up the GEDCOM file and repeat this process using a different email address (or after the merge removing ONE email address from your profile to use). See here for known issues regarding addresses/locations, maiden names, and more.
Additionally, note that you will have to spend a lot of time running the merge wizards if there are lots of duplicates. See here for concerns and suggestions regarding GEDCOM merging, tree merging, and more.