Without more info it's impossible to tell but from my experience possible explanations include;

1) Despwaned Night spawns will despawn at dawn if you are not present. I know this is an issue with wolves not sure if it happens with boars.

2)Killed The biggest culprit in this case is the grey dwarf shaman. Their cone attack can hit animals on the other side of a wall/door. Your pets melee attacks cant touch it but they will keep coming back to the range of the shamans aoe till they are dead. Solution is to have 2 walls.

3)Glitched Even if the game were not early access, which it is, stuff happens. Without specific information of your game state at the moment i doubt anyone could tell you what.

4)Other There may be other mechanics at work we dont know about.

Anyway, good luck with it. It is cold comfort but there will be more boars, and better.