Hello, Edwin. Unfortunately, the files can't be overridden. If there are living individuals from your files on WikiTree, all you need to do is make sure they are set to private. The red lock is the default on WikiTree for living people.
We try to avoid duplicates, but if you have some in your files, they are easy to merge. For instructions on how to do this, go to: http://www.wikitree.com/wiki/Merging
Following is what the Help Section says about updating profiles with new GEDCOM:
Can you update profiles with new GEDCOM imports?
No. You can add...individuals with new GEDCOM imports, but you can never update existing profiles this way.
There is no way to automatically "sync" WikiTree with other systems.
Our community is working on one set of profiles in one worldwide family tree. Automatically overwriting shared profiles would be unfair to other members of the community who may have been seeing these profiles in indexes and trees and making their own contributions.