So I completed the quest for Cesar to kill all the brotherhood members after doing the Elders quest for power armor via hacking their turrets. Well days later I went back to the bunker to get some Power Armor from their bodies and to my amazement almost all the members have responded. Is this suppose to happen?

Unless you blow the bunker then some of them will respawn when you return. Its not a bad way to have a regenerating supply of power armor to sell to the Gun Runners