To my knowledge, the chemistry involved with Prime treating water is permanent, it does not "revert" after 48 hours.
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When it comes to nitrates, nitrites and ammonia this is not the case according to Seachem: "Yes; Prime will detoxify ammonia, nitrite, and nitrate for 24-48 hours"
http://www.seachem.com/support/forums/showthread.php?t=3906
