Hi,
Thank you so much for your interest in our products and for using our community.
In MCSPTE1AK144, you can find a lot of documentation about this Development Kit, in fact the Getting Started with the S32K144 BLDC/PMSM Development Kit guides you step by step on how to use it with S32 Design Studio IDE for Arm and FreeMASTER tool.
In section 4.3 it specifies that you have to let the code run and then use Disconnect to avoid interference between the S32DS IDE debugger and the FreeMASTER tool.
I assume the latter is what is happening to you when using MBDT (Simulink) and FreeMASTER. However, for MBDT we have a specific community where experts can help you in this regard. Therefore, I ask you to please direct your MBDT questions in the following community:
Model-Based Design Toolbox (MBDT)
Hope it helps you.
Have a nice day!