Hi,
I'm only a DIY'er, so feel free to ignore!

The internal glazing, the sealed units, are not normally structurally integrated into the uPVC frames.
They are usually shimmed into the frames with expansion space all the way around.
With out the glass in, there may be some loss of rigidity to the frame, but that is all (although the shape of your conservatory will also help to maintain rigidity).
To ease your mind, you could remove the glazing beads around one of the sealed units (plenty of videos on YouTube about how to do this) and see how it has been shimmed. If there are no shims on top, you will probably be fine!