Glad to hear the main project is working well!
The SHM issue doesn’t sound like what we would technically call a ghost device. A ghost is a device that did exist on the network, was forcibly deleted, but its ID still shows as active in the controller’s device table. Those are reported just with a device ID, no name, and shouldn’t show up with any attributes at all.
Since in This case it shows up with different attributes, then it most likely has to do with the device handler which has been selected. It sounds like it is being treated as a multi sensor which reports both motion and open/close.
(My guess is this has to do with the smart home monitor feature where it reports on “all sensors” of a particular type. )
It may even be correct to have it show up twice under SHM if it has both capabilities. My guess is that in editing it, you left in the original capability and that’s why it’s showing up twice.
Since you were trying to edit a device type handler, I suggest asking the question in the developer category on writing device types, and people there can look at your code and help you fix it. We’re getting pretty far off topic for this thread. 
https://community.smartthings.com/c/developers/writing-device-types
By the way, you might want to take a look at Mike Maxwell’s very popular universal device type which is intended for exactly this kind of use case. You can use it to gracefully have an open/close contact sensor report instead as a motion sensor and all the other parts of SmartThings will work correctly.