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My alk and calc were bouncing around as well and caused some havoc on coral. I just adjusted dosing slowly to get proper levels; all you can do is wait it out IMO. Drastic changes will be just as bad for the coral.
I get what you're saying. I don't think you can ever get all the air out of the line but I try to get as much as possible. Looking at the line you can see huge gaps between air and liquid.
I see this happen if the solution is lower then the line in the container. I now make sure to add so this...