This paper examines the dynamics and control involved in the active removal of a large space debris-Envisat. In the light of European Space Agaency's e.deorbit mission, the current mission scenario consists of a chaser satellite, synchronising, capturing and detumbling the large uncooperative debris. A unique multibody approach based on floating frames is used to model the Flexible Multibody Dynamics. The controllability characteristics of a linear PD controller and an Incremental Nonlinear Dynamic Inversion controller are also studied. From previous research, it was found that in the docked configuration, the control of the system could not be achieved due to the complex elastic dynamics originating from the large solar panel of Envisat (14.2 m). This paper focuses on achieving robust control of this phase through advanced design choices in both structural and control aspects. It was found that the inclusion of structural damping and reduction of control limits, lead to a major improvement in controllability of the system. A basic digital notch filter did not prove effective for more robust control. This is because only a high order filter could account for the low frequency vibrations. Further, it also required retuning of the controller within the flexible model. These two aspects proved to be beyond computational capabilities. A simple control strategy of introducing a dead-band in control loop improved the control response considerably by allowing the disturbing frequencies to dampen out.