Have a similar set up with the cabin glass windows on my boat. I have to pull them every couple years to reseal them. They have a much bigger set in seat with with to achieve a seal, so it lasts longer, but they often leak. I have to keep it under cover to keep things dry in winter, and I am a fair weather sailor in the summer.
I see your problem, and can't come up with anything more than you have done. It will be too bad you loose the light coming in through it, but ya gotta do what ya gotta do sometimes. I hope some brilliant person comes up with something for ya. We'll see. Some smart people are on here.