In principle we do not support 'overwriting' an existing Team Server repository with the contents of another project. This can lead to all kinds of trouble with existing checkouts, branches, etc. That is why the Modeler does not offer such a feature.
However, if the repository of project B is currently not used and you just wish to replace its contents by project A, here's what you can do to clean it by hand:
You just deleted the existing contents of the repository of project B. Now you can upload the local project A to the project B repository and continue working using project B.