It shouldn't hurt the barrel to leave the pellets in from one hunting day to the next, or even from one weekend to the next, but be sure you store the gun in a dry location. Doing this raises some safety concerns. Always remove the primer cap. Be sure you know when your gun is stored loaded--I leave the rod in the barrel as a reminder anytime I leave pellets & a slug in the barrel. I don't think it would damage the barrel to leave pellets in longer, but for safety reasons, I never leave my muzzleloader loaded any longer than the few weeks of black powder season. I also unload and clean at the end of the day every time I fire it. You say you clean after every 3rd shot. I think you should clean before you put the gun away even after one shot. If you shoot 3 times in one day before you clean it, that's OK.