Adam,
Some people will say remove them because they are nitrate factories. Typically in most systems if you have enough circulation, live rock and live sand the tank will be somewhat self sufficient. I personally removed the bio balls from my wet/dry and kept the wet/dry as a sump and for circulation. If I was you I would remove just a few a week until they are all gone. Do it slowly so as to not create any problems. In my 70 reef I only have a UGF for my filtration and that is going to be capped off in about 1 month. I only did that because I have a plenum and wanted to the bacteria down there so that when I cap it off it will give it a true plenum setup.
Moral of the story..remove the bio-balls, but do it slow and maybe add another 10lbs or so of live rock and make sure you have good circulation.
--andy
