A distributed simulation platform, denoted as D-Sim, has been developed previously by our research group, which comprises three essential attributes: a general XML description for models suitable for both leaf and integrated models, a gluing algorithm, which only relies on the interface information to integrate subsystem models, and a logical distributed simulation architecture that can be realized using any connection-oriented distributed technology. The overarching research focus is to integrate heterogeneous subsystem models, e.g., multibody dynamics subsystems models and finite element subsystems models and to conduct seamlessly integrated simulation and design tasks in a distributed computing environment. A Partitioned Iteration Method (PIM) is proposed in this paper, which decouples the rigid body motion from elastic deformation of the simulated system using an iteration scheme. The method employs a CG-following reference frame for each deformable body in the distributed simulation of flexible multibody systems. The resultant simulation system can be used to integrate distributed deformable bodies D-Sim, while allowing large rigid body motions among the bodies or subsystems. It also enables using independent simulation servers; where each server can run commercially available or research-based MBD and/or FEM codes. Examples are provided that demonstrate the performance of the method and also how to decouple and integrate rigid body motion and elastic deformation using the developed gluing algorithm.