There is no (easy) way to automatically record "ondevice" in a way that persists after you disconnect the device. You can do such things in a plugin, but I don't know of one that does it.
The usual solution is to select all books and set the custom column to false using edit metadata (bulk). Next search for ondevice:true while the device is connected, select all and use edit metadata to set the custom column to true.
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