Mkv To Mp4 Batch Converter

Is there a way to do the following:
I am running Microsoft Remote Desktop to connect to a Win 10 system. I have used PowerToys on the PC to map CMD-C, and CMD-V to the PC equiv CTRL-C and CTRL-V. However I would also like to map CMD -W to CTRL-W. The problem is that the Mac grabs the CMD-W before the Remote Desktop app can map it and it closes the connection in the Remote Desktop app. Is there a way to capture CMD-W only when Remote Desktop is active and pass it to the app so that Power Toys Keyboard mapper can change it to CTRL-W?