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How are you measuring pH?
Did you leave your refugia running as you took everything out? If you disturb a sand bed with the system running you could let bacteria or other micro orgs into the system, this could result in stress to your system, and an increase ammonia.
If not, by taking out the lr and sand, you could have some nice de/nitirying activity taking place and by removing that and the algae, your tank's lr couldn't keep up with the demand. Again these are just possibilities, though I believe that bacteria populations, once established are pretty dynamic. Meaning, you've already got the cultures developed with more nutrients, they'd probably reproduce faster to consume them.
By taking algae out, I'd expect your pH to go down. That's a huge benefit of having a refugia, a higher, stable pH. I'd think that while the xenia would grow to consume the nutrients, it may not be as fast as the algae would be.
As far as PE, there are many reasons that sps exhibit PE: gas exchange, autotrophic feeding, heterotrophic feeding, shading.... we shouldn't be using PE as a measure of an sps' health.
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