Go to Device Management, select EZServe and do a SYNCH DEVICE. It sounds like the PLM link records were deleted by the factory reset (normal) and need to be restored. This should restore Scenes as they need link records in the EZSrve PLM and individual devices to function.
The link records have nothing to do with individual device control. Perhaps the missing link records have the PLM is a state where it can no longer communicate with the powerline after trying to run Scenes that are not defined in the PLM. After restoring the PLM with the SYNCH DEVICE unplug EZSrve again for 30 seconds to recycle the PLM. A simple Restart (not Reset) may be enough.