No need to shut a PT-6 down. The prop can be feathered with the gas generator running and the amount of thrust being delivered then is negligible for your purposes.
Run the check as JT suggests at a safe height and speed/flap combination representative of whatever you use to commit to take-off. The operative word here is 'commit'. Aircraft like Twin Otters don't have proper V1 speeds, rather a Take-off Safety Speed which is typically reached at about 50 feet. Certainly the speed that you would typically lift off at would not be a safe speed for simulating an engine failure.
Pilots have trained safely on Twin Otters and the like ever since they were built. But safe check & training pilots are always conservative when simulating engine failures.
Don't accept any heroics pulling back to zero thrust before take off safety speed and at least 50 feet has been reached. Know your book Vmcg before trying any rejected takeoff practice.
Pulling power all the way to flight idle at low speed in the air is a recipe for disaster. Do not do it...ever. The aeroplane has an auto-feather system which is so unlikely to ever fail when needed that it simply does not justify training for that possibility. If your Regulator or anyone else insists on pulling to idle at low speed either throw him off the aeroplane or get off yourself. Or go to a proper simulator.