How to differentiate between 2 Micros on Linux
The USB VID, PID and Serial Number are all programmed into the chip when you upload your sketch.  The VID and PID are tied to the board, and the serial number is always the same regardless of which board.

So no matter which board you program it will get the same details as any other board of the same kind.

There's no option to change the serial number (there is, IIRC, actually no serial number defined) but the VID and PID are provided as a pair of macros on the compilation command line: USB_VID and USB_PID.

So you could (cheakily) create a new board definition (based on the existing Micro one) that is "The other Micro" and provide a different (unofficial) PID to that board.  You can then differentiate the two boards in udev using the VID/PID combination.

Of course, you have to then ensure that you have the right board selected when you program them, and the act of entering the bootloader on the "other" board would revert back to the old PID which is programmed into the bootloader, but I'm sure you can cope with that.