Originally Posted by BBL_Brewer
Just up your boil volume a little to compensate and adjust your gravity accordingly.
This. Some software has a hop absorption factor you can use, but I usually estimate about an extra quart per 4-5 ounces of pellets. Seems to get me pretty close most of the time. I enter it in BrewTarget as kettle to fermenter losses, so I just have to tweak my equipment profile if it's going to vary significantly from that standard.