If the stepper driver overheats you should miss multiple steps (large shift). The stepper won't skip steps due to overheating. It will go to 80 or 100 C before it starts to degrade. If it doesn't burn you it's OK. The other causes of skipped steps are too much friction or too much acceleration. So try lowering acceleration settings.
Also check for friction and stiction. Uncouple the belt and run the axis back and forth by hand. You shouldn't feel any friction or grabbing. If you do then rethink your bearings/bushings.
Also check for friction and stiction. Uncouple the belt and run the axis back and forth by hand. You shouldn't feel any friction or grabbing. If you do then rethink your bearings/bushings.