If I go 35 mph on a 50cc scooter will I kill the engine?

Not necessarily. It all depends on the transmission and gear ratiOS. The higher the gear (4th, 5th, 6th etc.) the faster you will go, but the less torque will be getting to the wheels. So you might run out of horsepower to overcome the wind resistance etc. It's like riding a 10 speed bike. Easy to go up hill in first gear, not easy in 10th gear. The pedals are moving faster in first gear, but more power is getting to the ground and it just takes longer to go a distance. With your scooter, you might be making the engine go very fast at 35 mph, even in high gear. Most of those engines have a governer attached so the engine can not red line, but sitting here, I can't guarantee it.