Many heat pump air handlers will have electric strip aux heat. Code requires that these be subdivided into loads less than 48 amps (and since heat is continuous, 48*1.25 = 60A for the max breaker for heat).
So you could have more than 48 amps worth of heat, and someone decided to keep one off to save money (and the house will heat much more slowly on cold days).
Or perhaps you don't have much aux heat installed and that second breaker is not feeding any heat strips. In that case, turning it on should not affect anything.
See if there is a nameplate rating on the air handler which tell you how much strip heat is installed in KW or if there is an MCA number on its nameplate.
You could also look at your breaker panel and see how many circuits feed this heat pump. One large one 80 to 125 amps) would make sense for two 60+60 breakers. You could also have two breakers, one landing onto each 60A breaker in the air handler. If there is a single 60A circuit, it probably lands on one of the two breakers in the air handler and the other has no power applied to it.