If you use the window handle of you main window, then it might indeed be that you are blocking this messagepump. That’s why people like @Dragonlaird use an approach with a separate (hidden) window and pass this handle to SimConnect instead (see this post).
My application is intended as the basis for a kind of a Hardware hub, which is normally going to run in the background anyway, just offering some features for monitoring and testing during development. That means that I’m not so afraid of the blocking of the window for a while. But if it would really get annoying, then I would go back to the “separate message pump approach”.