I was thinking about putting something on the drain into the bottom sump (IE: filter floss, silter sock, etc), but that defeats the purpose of the top level refugium for food production, and also add a failure point if the filter floss or whatever become clogged and eitehr floods the bottom sump (of backs up and floods the top one).
The bottom sump is a 150g sump, so I would need to get another water container for the impending water change after draining it to vacuum it. I have used the wet/dry vac in the past on other tanks/sump and do agree that it is fast and effective. I just don't know if I want to try using it on this setup or not (especially since I don't know for 100% assuredness that it is what is causing our problems). As with the other suggested resolution steps, if I knew for positively sure that it was what would resolve our problem, then I would bite the bullet and just endure the "pain" and get it done. So far I can't nail down the exact root cause, so I am going after the "low hanging fruit" to see if any of it helps the situation. That plus right now we have less and less time to dedicate to the tank. Hopefully that will open back up in a month or so. Until then we dedicate enough time to maintain it, just not truly "improve" it (at least not in my mind).