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the bacteria in a brackish setup is the same as a sw setup... so either way, the bacteria currently in the filter on the brackish tank wont do anything for you in the fw tank
What I will most likely do is run both filters on the 29g for a month or so. I am no real hurry because I am turning the 40g into a pretty wild looking paludarium. I was just wondering if I could go from BW to FW like that.