Being that a Pagoda Cup is kind of resilient, I would just dip the affected parts in straight Peroxide for a minute or so. It will make this coral upset for awhile, (PO) but like mentioned before it will bounce back. (assuming everything else is ok) Good luck!
If algae is growing on the coral it's probably dead or dying. If it were me I'd clip it off. I'm so paranoid of doing dips for fear of killing the coral.
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