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Give them time, I had the same thing happen to a colony that I have. Got a little aggressive pulling the GHA off that was overgrowing it and beat up the polyps a bit. A few are very small now, but appear to be getting bigger. Just like new baby polyps that start off small, they should get bigger.
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My build thread:
http://reefcentral.com/forums/showthread.php?t=2548422
Current Tank Info: 65 gallon mixed reef, Eshopps sump and HOB overflow, RO-110int skimmer, Reefbreeder 32" photons V1.
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