So here is what finally that worked for me:

1. Find the amount of time it takes to finish all the activities on the onTimer() routine using millis().
2.Just before EPROM.commit()
stop the timer(hw_timer_disarm(void))
Optional: detach interrupt
Depending on what you found in step 1 above put a ...

On the same boat....but have a temp workaround:



detachInterrupt(interruptPin);

EPROM.put.....
EPROM.commit();

delay(2500);
attachInterrupt(interruptPin, ISRroutine, RISING);