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When I did this, I had chaeto and caulerpa in the main tank. After I felt the dinos were "totally" gone, I yanked the caulerpa and gradually moved chaeto to the Fuge, or other tanks.
Odds are this isn't your issue, but invisible chemistry holds surprises... Just because you are throwing food in doesn't guarantee your parameters are what you think they are. Let's figure if there's obvious reason why your algae stopped growing.
You likely have both abundant N (nitrate dosing) and P (flake food tends to be out of balance on the P side - which is handy) but check N, P, Alk, Ca etc and post. If those all check out, then you possibly created a trace element limitation.
For cyano, if that's what it really is...Then peroxide is my go-to. cyano is affected at 1/10th the h2o2 concentration of other classes of photosynthetic stuff, so start low and adjust up until you see effect likely around 1ml/10Gal. I also target the cyano patches with the peroxide. I see no reason to play fair.
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