Sorry to hear about yor losses!
I can honestly say I've never had anything like that happen. Could it possibly be that the algae is causing denitrification? Since it stores some nitrates it could store them long enough and act live a substrate does in the ocean, basically breaking it down into ammonia and not fully into nitrogen gas. Then when you disturb it, it releases the ammonia in small amounts. That might explain why your smaller fish die Shelley. And possibly when a large amount of algae is disturbed, like in an algae scrubber, the larger fish die to.
If I'm right, then I would try turning the ball valve off for the drain and taking the algae out for cleaning, then sucking all the extra water out of the algae scrubber and testing it for ammonia.
Just an idea though!
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