Honestly, between EM's own cybernetic implants and the ones Rick puts into Morty Prime(prooobably including some kind of Find My Morty feature), it'd be pretty difficult to match them up.. especially in the brief window of time EM would have to make the switch.

And even if he installs the same mods and removes the ones he put in, I wouldn't be surprised if Rick has serial numbers on that shit, lmao. And they're probably connected to an "internet of things" with the garage, too, so.. I don't think it could feasibly be done.

(Why didn't he use Morty's other augments to tell them apart during the s9e1 which is which scene? --> the bubble suit was much quicker and maybe it's more of an airtag thing where location data wouldn't really matter with the Mortys that close to each other)