Hi fishx65,
Depending on the "R2" you are using, 2 hours may not even be half-way through the discharge.
Pretty much any R2 flashlight or module that supports 2xCR123 cells or 1x18650 cell, use a buck style regulation circuit. The regulation circuit has some over-head voltage requirement to run the LED in regulation.
Fresh off the charger, these types of lights will be at about 50-80% of their normal maximum output on the 18650 cell, (keep in mind, that since LEDs maintain pretty consistent color temp, even a full 50% difference in output is not always obvious unless compared side by side). As the cell drains, the output does diminish, but after 2 hours, it's probably only down about 20% from the initial brightness, the result is that it still appears to be at maximum brightness, but it isn't...
Since the LED is being driven with less "oomf" than it would have been on CR123s as the power source, the runtime is often increased to double or more what it would have been....
*disclaimer: the above information does not apply to ALL flashlights that can accept these 2 battery types, for example, the T100C2 from EagleTac maintains regulation through most of the discharge on either power source as a result of the regulator design having remarkably low over-head voltage requirements combined with hand-selected low-Vf LEDs and slightly lower set drive levels than normally associated with the "high" setting on many modern Cree flashlights (has to be lower due to the small form-factor XPE used)..
Anyways, that's probably enough rambling, either I've just thrown a total monkey wrench into this, or you have some insight into how your flashlight works.... Either way,
Have Fun,
-Eric