Importing a Gedcom file to your family site, does not replace a previous Gedcom file, it adds a new one to your family site.
Each time that you publish a family tree to your family site from Family Tree Builder, if you leave the name of the project the same, then the publishing will replace the previously published version of the project.
I see that you only have a web tree on your family site at this point in time. This means that if you either publish a tree from Family Tree Builder, or import a Gedcom tree, it will create a new tree on your site.
In order to view all your family trees on your family site (those that you made online, those that you made in Family Tree Builder and published online, and those imported from Gedcom files) so that you can edit or delete a tree: go to Family Tree > Manage Trees.