Bluetooth Device Shows Up In Menu But Not In Preferences
I just had this same issue (device shows up in Bluetooth menu bar but not in System Preferences pane) on OS X 10.10.1 after replacing my iPhone, but I found another way to remove the old device, without editing or deleting the plist file.

Many system menu bar icons support advanced menus if you hold the Option key when you click them (for example, choosing an AirPlay device under audio, or seeing wifi modes and noise for your current network).  When holding Option and clicking the Bluetooth icon, there is extra information including my bluetooth hardware address, a "Create Diagnostics Report on the Desktop" item—and each device's submenu has its hardware address, signal strength, and a Remove button.  Worked great, no reboot required!