We could see that what brought Emeth back to life was Luffy's unique heartbeat. We also saw that he wasn't sure if now was the right time for him to act.
We know that 200 years ago, he climbed to Marie Geoise, started fighting and then just stopped all of a sudden.
I think that 200 years ago, someone with Luffy's fruit reached gear 5, began to attack the gorosei, so Emeth followed, and then they killed that fruit user, so Emeth was immobilized again. After taking care of the real threat, the gorosei didn't care much for Emeth, they gave it to their scientists to dismantle, believing they had obeyed. Also back then, Emeth did not carry a transponder snail on him, transmitting all of the government's secrets to the world, so they didn't consider him as big a threat as now.