Electronic – STM32: Timer encoder reset

As you've discovered, handling counter overflow with an interrupt handler is tricky and race-prone. Even with your priority boost, you'll get the wrong answer if interrupts are disabled while you read the counter. There's a much simpler technique which works if you're not reading the clock from interrupt context (note that I'm using the DWT cycle counter here, which is built into the processor thus fast and simple):

uint64_t last_cycle_count_64 = 0;

// Call at least every 2^32 cycles (every 59.6 seconds @ 72 MHz).
// Do not call from interrupt context!
uint64_t GetCycleCount64() {
  last_cycle_count_64 += DWT->CYCCNT - (uint32_t)(last_cycle_count_64);
  return last_cycle_count_64;
}

If you need to call it from interrupt context (or with a preemptive OS):

volatile uint64_t last_cycle_count_64 = 0;

// Call at least every 2^32 cycles (every 59.6 seconds @ 72 MHz).
uint64_t GetCycleCount64() {
  uint32_t primask;
  asm volatile ("mrs %0, PRIMASK" : "=r"(primask));
  asm volatile ("cpsid i");  // Disable interrupts.
  int64_t r = last_cycle_count_64;
  r += DWT->CYCCNT - (uint32_t)(r);
  last_cycle_count_64 = r;
  asm volatile ("msr PRIMASK, %0" : : "r"(primask));  // Restore interrupts.
  return r;
}

You may need to enable the cycle counter first:

DWT->CYCCNT |= DWT_CTRL_CYCCNTENA_Msk;  // Set bit 0.

I've found the issue. It turns out it is not possible to trigger off the same pin on multiple GPIO ports. I was overwriting my PA3 interrupt with a PB3 one.