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Just put an airstone in the new water for a day before you put it in the tank - should have a similar effect to the surface agitation you have in your tank and reduce all dissolved gases to their natural concentration.
I don't think you can get co2 to dissolve into tank water through surface...
Mulm is so heavy that if you syphon a bucket out and leave it for 5 minutes you can syphon it back in and leave the mulm on the bottom - but this necesitates a) having somewhere higher than the tank to syphon down from, and b) being happy to lift buckets of water. Looks like it's floss for you...
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