That "Only owner can damage" config option works fine, but another plugin must be changing the heli owner after a certain time. Loot Defender used to do that, but it should have been patched a while ago, do you use that plugin? Is it up to date?
with heli HP, you should also scale the rotor health otherwise people can still kill the heli easily. 10k HP with 900/500 rotor health is vanilla. If you doubled the main HP for example, you should also double the rotor health, so ex: 20k HP, rotor HP should be 1800/1000.