The UVMM addon includes four invisible vessels with two for adding mass to vessels and  two for removing. It's very simple in nature but powerful. You'll need the Universal Cargo Deck 3 by Yuri Kulchitsky to attach these to ships that you want to alter the mass of. Read the included readme file in section 1 and 2 before usage. As improperly using this addon can cause Orbiter to crash. For a quick test take some ships for a spin in the included example scenario. To install unzip UVMM into your Orbiter root directory.