I milled out a double-sided PCB board last week using the amazing features in ChiliPeppr from https://github.com/ameennihad/widget-eagle that allow you to easily flip your board over.
I did find, though, that on the flip the Y was aligned perfectly but the X was off by a couple mm. I still haven’t quite figured out what happened. I was able to re-align visually and proceed with a successful board.
+Ameen, if you’re over on this thread. Do you have ideas?