I've had SAMD21 boards from sparkfun "stop working" due to something going wrong with the host side.
Double-tapping reset doesn't put the board into upload mode, nor does host-initiated uploading work.
Power cycling the USB hub that the board is on fixes the problem! (presumably rebooting the computer would work, too.)
(I have no idea whether the pro-micro has USB logic in its bootloader that might cause similar behavior, but it's worth a try.)