Yes you are correct........minus the count in the timer......I most often use this scheme where there is an output compare circuit that generates the interrupt so the process is a bit simpler to program.....just add new period expiration time onto the previous output compare interruot time.....but the other scheme can be done too...just reduce the new interrupt time by the time in the counter that occurred after the overflow queued the 49 mSec interrupt while the processor was off executing the latency period.
Michael Karas