No, I understand what I'm doing. But thanks for the insults ;~)
If I get a motor interrupt while in the middle of a PID calculation in my temperature control ISR, by the time I service the pending motor interrupt, it will be too late (motor will have moved).
So I'll turn off the temperature control interrupts to prevent that. Similarly, I may need to turn off the motor interrupts so my sample timing is deterministic (so I can implement good digital filters).
It looks like I can just reset the appropriate bits in the mask registers (TIMSKO and EIMSK for the timer and external interrupts, respectively).