your right, it doesnt matter if the rock is in the sump or display, it filters just the same......anytime live rock is exposed to the air, it
will cause die-off of the bacteria....its the main reason a tank cycles when you bring your rock home....you can minimize this by keeping the rock in saltwater while you are working on the tank, but there
will be a cycle of some sort....might be small and barely noticeable, might be larger and troublesome......kinda the risk you take when you mess with the tank
....just try not to doddle too much and get er done as quick as you can
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260g mixed reef, 105g sump, water blaster 7000 return, Bubble King SM 300 skimmer, Aqua Controller Jr, 4 radions, 3 Tunze 6055s,1 tunze 6065, 2 Vortech MP40s, Vortech MP20, Tunze ATO, GHL SA2 doser, 2 TLF reactors (1 carbon, 1 rowa).
http://www.canreef.com/vbulletin/showthread.php?t=50034 . Tank Video here
http://www.vimeo.com/2304609 and here
http://www.vimeo.com/16591694