Your file is too big but I was able to recreate the situation with a much simpler model. The windows are written into the IDF model correctly and you would see this if you opened your model in OpenStudio GUI or the IDF Editor. Or, if you requested surface-level outputs from the simulation, you will see that there are results for the windows.
The reason why you think that the windows are not written into the model is because the Import IDF component does not import the newer format of window objects for the newer version of E+. I will also highlight that this Import IDF component is under the WIP section for good reasons and it is a far cry from being able to import most of the content in IDFs (especially across different versions of E+). So please take everything that this component does with a grain of salt and don’t rely on it in the same way that you would for the non-WIP components.
Also, if you are going to use this WIP component, also please check the readMe! output where you see that it will tell you that it fails to build the window surface:
All of this said, I have updated the component to read the newer window object format of E+ so that you can now use it to check your geometry from newer versions of E+: