rinsing your biomedia with
tap water wont kill the beneficial bacteria

some get removed in any type of rinsing, even in the currents inside a filter. but the base slicks are there/producing more
perhaps soaking it in
refreshed tap water for days might lower (not sterilize) the bacteria count, but not brief rinsing. Too low contact time.
Tap water is an inoculator of bacteria, not a sterilizer. When we make lemonade fresh out of the tap, the little black ringlet gasket at the exit faucet is depositing thousands of colonies of various bacteria, nitrifiers included, into said drink. All the hot and cold running past it didnt sterilize the gasket, it inoculated the plastic with bacteria and bio slicks.
I hear the only way to kill them is with an alcohol additive + salt ring concoction lol but yep rinsing is ok, even tap rinsing.
Old school freshwater aquarists already know and implement this trick in refreshing the old sponge filter weekly/monthly. we don't use our good drinking water for that. Using tank water is ok, but not required.
-whether or not bioballs are needed at all is debatable-
they're needed when removing them would cause a backup in ammonia processing. All they do is contribute to standard nitrification, this occurs even if we don't keep them because surface area in the reef tank is abundant even without bioballs. They're also decent oxygenators (the delivery and pumping/ splashing on and around them is the oxygenation) but again reef tanks are not notoriously low in 02. to use them is not harmful or we'd have never made it past the 90s with live coral.