Keeping a decent sized tubastrea is going to be tough in a Bio Cube, you need to feed it too much. IME nitrate is usually the culprit with big valonia outbreaks, this matches up with what you've been seeing.
Consider what your situation is going to be post removal if you go after it now, all that nitrogen is going to end up feeding something and you probably won't like whatever it is. The valonia is comparatively easy to manage. Get the nitrate issues solved before you start removing the valonia aggressively.
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