I am having this problem on VW 2023 SP2. I made changes to the window style (just data info for a schedule) and different (style) windows on a different wall now don't cut through the wall. Actually, I then changed the style of one of the windows and THEN that wall wigged out. I tried moving it, copy/pasting, re-oping the file, placing new windows in the wall also have a similar result. I just did a test by making a new wall and it looked right initially but then did the same thing.
It appears if I break the wall up into segments (one for each window) it fixes it... now I just need to cover up the extra lines showing up in the elevation...
Of course this is happening on a final deadline. I guess I can be happy it's one one wall.