Water quality issues with one tank system

gradstudent1

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So I've posted here before about my experimental system for my thesis work (seen here: https://www.reef2reef.com/threads/temperate-coral-research-tips-for-tanks-coral-maintenance.593285/), and I wanted to get some input from the community.

I'm doing research on a temperate coral species, and have collected some samples a few months ago. They've been doing VERY well in this single system, even spawning at one point in August (let's call this system 1). However, I have another system running parallel to it that doesn't have anything living in it, just artificial seawater circulating (let's call this system 2). I take out my coral samples and place them into system 2 to clean system 1 of algae from time to time, and these corals get very stressed when they get placed in system 2. Should I go ahead and completely drain the water out of system 1 and just pump it into system 2 to get similar water quality? I'm eventually getting more samples in soon and would like to have similar water quality so that I can space them out between the two systems - don't want any of them stressed for other reasons before my experiments begin.

Thanks!
 

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