Because it decreases population variability.
Since it became extinct, it probably wasn't essential but this allele could have been useful under certain circumstances. If enviroment changes population with less variability, has smaller chance to adapt.
We have flower with allele A (adaptation for cold) and a (adaptation for hotter climate).
In cold climate there will be more individuals with AA or Aa because they will have bigger chance for survival than aa .
If allele a became extinct (there will be only AA) and climate is still cold nothing wrong happens. But when climate gets hotter population with only AA will have smaller chance for survival.
On the other hand if there were still individuals with Aa, abundance of phenotypes would have changed (more aa or Aa) according to the change of climate.