Ehhh… so did Neo. The machines let Smith overwrite him, so they could fry that iteration.

The machines likely had their engrams saved, and definitely had their bodies. Clone 'em, stitch ‘em back together, homunculus them, whatever. There was a big ol’ time skip between Revolutions and Resurrections anyway.

Especially since “Neo” had been through however many cycles before according to the Architect.