There are probably things on ships that can't be replicated, though. A sublight shuttle may be easy enough, but replicating the dilithium and antimatter needed for a warp capable vessel harder. Also, replicators may only be able to manipulate protons, neutrons, and electrons... fine for making everyday objects, but inadequate for certain components that use more exotic particles.
I don't remember if the shuttle the Protostar replicated was warp capable. If it was, the VR was probably designed to beam in some of the mothership's antimatter and dilithium.
I don't remember if the shuttle the Protostar replicated was warp capable. If it was, the VR was probably designed to beam in some of the mothership's antimatter and dilithium.