That doesn't sound good. Did the GCS ever connect correctly, or were you just flying with quad default settings?
Did you do something that might have caused this (install Cleanflight, upgrade from OP to LP, etc.)? Many quads come with an old version of OpenPilot and that is not compatible with the current version of LibrePilot.
You could take the CC3D out of the quad and look at it with a magnifying glass; looking for cracks in the board or damaged traces or missing components.
You could try reflashing, starting with the SBL bootloader flashing procedure, then firmware flashing using GCS and manual method.
If it were me, and I didn't mind wasting $10 - $20 to get flying sooner, I would order a replacement CC3D, and get it coming in the mail while I tried other things.