I think that you made a mistake by setting up your own CVS server. Version-control at a corporate level falls apart pretty-quickly when there are “sattelites.” I think that you needed to fork off your own branch, but that you needed to do so within the auspices of the version-control server (and system) that already existed in your organization.
Not-every branch “survives.” Not-every branch ought to. “Branches” do not have to be “functional.” If you spin-off a part of the development effort into a version-control system that is entirely disjoint from the one that the enterprise as a whole is using, I fear that you will completely negate all of version control's benefits....