My first question. Is there wet brook also below the excluder?
Your queen may have moved up during your last inspection.
Do you have a top entrance? Your gueen may have walked out the front door and into the top entrance. A good very experienced beek friend documented it happening to her.
Look at the brood in both areas. Look for eggs, if you find them, the queen has been on that frame within the last 3 days. Is there wet brood, if so, the queen has been on that frame for 3 to 9 days. If the brood is capped, she was on that frame, within the last 10 to 21 days.
If you have eggs in both the top and bottom boxs, you probably have 2 queens, mother daughter laying.
If the brood turns out to be drones, you have laying workers above the excluder.
Jim