The big thing is just that the change happens slowly. Are the ones that are in the main tank appearing okay? I don't know if they will be good in the long run or not, but if they appear to be acting normally I would say leave them there as that is less of a hardship than moving them back and forth which will just shock them repeatedly. I know one thing to look out for is an outbreak in disease in the ones that you put in. I had a ph swing caused by a water change and had an outbreak of columnaris afterwards. Whoops.
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