during some simulations I deleted the windows from a few external walls but they still remain in the 3D view. Restarting the project doesn't help. Overwriting other windows on top of them makes them look opaque.
I deleted the windows from the project browser by right click - delete function.
The project is attached.
experimenting with windows.dgn
And also, I see that you've worked with plenums in this model. I would not suggest you creating plenums as they do not have any significant effect in your design, and have detrimental impact on Part L or ASHRAE assessments (by increasing number of rooms and surface area). If you really wish to have a cavity above your room, you can do the same by creating a hole in your roof slab as suggested in this article.
Thank you for the suggestion about the plenums, I use them often.
My actual version is:
Link to the workspace:
Thanks for letting me know.
The latest build is 10.09.01.38, which should be available here. see below:
However, I can not download the file you shared through the link, would you please create a service ticket through the link here, so that I can have your projrct through there?
And, I am quite confident this is happening due to unexpected presence of plenums, hence I would request you to do this without a plenum.
If its still happening weird, I would wait for your service ticket.