Hello and welcome to the forums Cram,
It is not clear exactly what you are trying to achieve here.
At the point that the overflow isr would occur the MTIM is already reset by itself reaching the modulo the counter is set to.
As for trying to jump out of the middle of an ISR to somewhere else, this is definately a no-no. You should mark that something occurred and then fall back to the normal programme flow where you would act appropriately considering that this event has occurred.
It would seem that as you are not really going to achieve anything within the ISR here (as MTIM already reset) that simply polling MTIM:TOF might be the best solution.
Or maybe I have missunderstood what it is you are trying to achieve.