@soren Sorry for the late reply. Atom currently always copies the top option in the list. If there is an actual Pycom serial detected, it will place that one at the top. Anyway, this is just a result of your issue, not the cause.
So just to be sure, after rebooting your mac, you are able to connect to your device? Then when switching out to a different lopy, the comport disappears from the list of serials, even when closing the connection during the swap? Do you switch expansionboards, or just the lopy? You could even hot-swap your lopy while keeping the expansion board connected, see if that helps.