Yes, you recalculate the stress boxes. Often the stress boxes that are only available sometimes are noted in brackets. For example, a character with mediocre endurance in human form and great endurance in wolf form plus supernatural toughness. I would write that down like this:
OO (OO) (OOOO)
So the first two boxes are always active, the next two boxes are from the increased endurance, and the last 4 are from toughness and therefore subject to the catch. Some people only make one bracket, I suppose, but I like the distinction between increased skill and toughness powers, so I know where to apply the catch.