Looks like you are planning to alter the reload value of the interrupt generator on the fly.

To avoid getting into complicated issues like "at what point of the machine cycle the reload will happen" etc, would it not be a better idea to disable the timer interrupt when re-loading ? At least then you know the fixed number of cycle delays and that can be compensated in your re-load value.

And depending on the MCU oscillator which again depends on the crystal accuracy for an RTC, may not yield accurate results - unless some kind of software calibration is done periodically.

Raghu