I am so sorry you are getting conflicting and confusing advice.
One glider is sick with giardia - both gliders are being medicated, which is causing them to feel "off" and stressed. One glider is picking on the other, causing even more stress, especially for the one being picked on.
In my opinion, if you feel he is causing more stress by picking on her - then put them in separate cages. Even if for one night so they can get a rest from each other. I certainly wouldnt wait until one of them is at the bottom of the cage.
It is your call,You are the one who knows how they behave when they are well and you are the one who is witnessing what is going on with the two of them and should be able to determine if its bad enough to separate them for one night.
Again - what an awful thing to be going thru.