Why are Fortuna entropy pools reset after a reseed?
If nothing else, it makes the output of the pool irrecoverable. One of Fortuna's goals is to make prior Fortuna outputs safe from a compromise (the discovery of all of Fortuna's current data by an adversary). If the pool continued on without a reset, with little or no entropy added before the compromise took place, the adversary could more easily calculate the past contents of the master pool.

Edit: Per M. Grieu (Merci!), let's make that "more easily verify guesses of past inputs to the master pool".

Also, I believe the OP's question is less about LibTomCrypt than about the Fortuna algorithm itself.