Maybe your file data structure got damaged somehow and a reference remained in it to a Window that does not really exist in 2D.
I would try this (may not work but worth a try):
Show only Walls and Windows in 3D.
Then I would delete half of the Walls and see if that deletes the ghost Window.
If yes, then I would then delete only half of the half that resulted in the disappearance of the ghost Window.
By repeating this having thing we can get to the Wall the Window is connected to.
This of course assumes that the Window is attached to a Wall logically within ArchiCAD as all normal Windows do.
If you found the Wall the deletion of will get rid of the Window then you should probably just delete it and recreate it.
This way you can get rid of the problematic element that created the phenomenon.
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