You only remove the Bioballs if you can replace the biological filtering that they do for you. I converted over to a DSB and live rock and they are now my biological filter in place of the bioballs. The bioballs are a nitrate trap in that they collect tank garbage as water flows over them and it breaks down into eventually nitrates. They do absolutely nothing eliminating nitrates but just contribute.
When I was FO with bioballs, my nitrates were usually over 60 and once your tank gets around two years old, the nitrates are hard to control as the bioballs are rather filthy. I am slowly removing all of my bioballs as my DSB and live rock take over. My nitrates now stay at around 5 or less due to the denitrification properties of the DSB.
If you have enough live rock and sand and want to remove the bioballs, do it slowly over time. I remove 10-12 every weekend and have had no problems. They will all be gone in another week or so. If you must rely on bioballs for your biofilter, you can rinse about 1/3 of them a month to get rid of the garbage collected on them in salt water from the tank. Don't rinse them all or you will get rid of all your beneficial bacteria. The easy way to do this is keep them in three separate mesh bags or use three different colored bioballs.