It is possible to program a new value to a timer counter register at any time. However if you just change one byte of a 16 bit counter you may get strange behavior it an increment event comes right after the software load.

Also note that you should study the data sheet, users manual, and family architecture guide carefully regarding the timers on your particular processor. Many of the timer designs have a defer mechansim built into them that make the timer stop counting when one of the two bytes is written and will hold the timer stopped until the other byte is written.

Michael Karas