Eclipse adds to the creature's base attack, but doesn't change the base attack itself. Burrow, on the other hand, actually changes the creature's base attack. If you burrow a Pest with an Eclipse out, the burrow halves the base attack, not the 2 attack. So there is no way you can abuse any kind of weird timing loopholes by doing a burrow/Eclipse/unburrow trick to try to get a 4 damage Pest.
Antimatter takes the current attack, multiplies it by -1, and assigns that number to be the new base attack. So when your Pest becomes antimattered, its new base attack is -2, not zero. But when Eclipse is removed, your Pest loses another 2 attack, because the initial gain of 2 was lost due to antimatter.