Is the "BD Remote Contol" device showing up as paired - or actually as _connected_ when you press buttons on your remote?

A device is _connected_ when its name is displayed in a bold font in the menu of the OS X Bluetooth menubar item and you are offered the option to "disconnect" it.

If the Harmony Hub for whatever reason no longer connects to your Mac via Bluetooth, the only way to re-trigger Bluetooth pairing is via the Harmony app on your smartphone (follow instructions in point 3 of the FAQ entry to re-establish it, instructions in point 4 if the device shows up as connected, but nothing happens (which is what you get when OS X holds wrong information about the device in its cache)).