Once your gedcom is uploaded, the next step is to review each person in your tree and re-link all their family to them. Start with yourself first and work backwards in time. The links consist of ((lastname-codenumber)). Once this step is completed for all of the names in your gedcom file, then your family tree will be working again.
I refer to the watchlist alot. It can be found at " My WikiTree/Watchlist ". It lists all the peoples/profile names in your gedcom. Hope it helps!