Increasing complexity of systems and software in the automotive industry, coupled with distributed development environments has intensified adoption of Software in the Loop (SIL) systems, i.e. setup where traditional hardware components are designed and tested in pure virtual PC/IT environment consisting of virtualized hardware and networks. Cloud-based SiL simulation systems involving multiple contributors and orchestrators create huge risks for organizations due to potential for leakage of confidential model-IP to adversaries within the distributed infrastructure. This can create a bottleneck for wide-scale adoption of SiL-systems. We propose a data-flow architecture using trusted-computing technologies (e.g. Intel-SGX) to protect models and IP in cloud-based SiL environments. We illustrate that these protections can be designed to be compatible with existing SiL tools and workflows with minimal modifications. Further, we highlight the need for future standardization efforts of such security architectures in the SiL domain.