Bio balls are smooth non porous media to which nitrifying bacteria and dissolved organics attach. The bio balls in a trickle filter are providing the ideal environment for nitrifying bacteria and therefore that is the best nitrifying filter that anyone can provide. However as they are not porous and denitrifying bacteria can not get below their surfaces to an oxygen free environment they can not survive therefore they do not exist. Therefore the dissolved organics are quickly turned into nitrates which enter the water stream, in addition a scum of dissolved organics adhere to the bio balls and this is high in nitrates. This can not be denitrified as no denitrifying bacteria exist so after it builds up for a while it sloughs off into the tanks water causing an almost instant spike in nitrates. If the bio balls are under water instead of out of water with water being trickled over them, they will have less denitrifying bacteria on them and they will be less effective at nitrification, but they will get even larger layers of scum build up even quicker that will slough off into the tanks water more often. Using live rock rubble will provide the same effect as live rock when under water, but will provide less effective nitrification then bio balls when used in a trickle filter system as there is less surface area for the nitrifying bacteria as the pore spaces on the live rock quickly become clogged with organics. They will not support denitrifiers when used in a trickle filters due to high oxygen levels so they will slough off scum of heavy nitrates just like bio balls. Hopefully this is not confusing, it is concise. As suggested above, just remove them a little at a time, but do remove them as with the small bio load you have in your tank your live rock system will handle the load. However, the change should take place over a period of weeks to be safe. If you are planning on adding more fish I would consider adding more fine sand or dead rock as a media for bacterial growth. Either sand or dead rock will become live soon enough that you will be able to make small additions a few weeks after the bio balls are gone, if you put the dead rock or sand in before starting bio ball removal.
