If you haven’t already, upgrade your Java to the latest Oracle Java 1.8.0_101.
Without the correct cert trust relationship which is why you need to upgrade your Java, your openHAB instance cannot talk with the my.openhab servers so none of your Items will show up.
You can have multiple .persist files and use multiple .persist strategies. See:
The big question is what is in your myopenhab.persist file? You have to define which Items get shared with my.openhab in there.
It’s the same issue. Without the trusted cert which comes with the new Java your openHAB instance cannot talk to my.openhab.