I would remove the pellets if unused for several months! Any humidity over that period of time has the potential to kill your pellets with moisture regardless of the cover, it may be waterproof but not humidity proof! Specifically any pellet dust can be a killer over time to an auger. It can setup like concrete jamming the auger tight. Remove the screw on the trap door to the hopper with a bucket under it to catch the hopper pellets. You my need a ruler or slim paddle to move pellets to the exit door. After that is done, remove the ruler/paddle, then power up your smoker and press and hold the prime/smoke button letting the auger empty any remaining pellets into the burn pot. Once completed turn off your smoker and empty the burn pot.
