OK, I found a way, and it makes perfect sense.
Run HDHomeRun Setup program. On the first tab, "Configuration", is a list of devices and their status. A good device should have status "OK". A removed device would have a status of "Not Found". Click the Source Type drop-down list of that device. The choices are "Digital Antenna", "Digital Cable", and "Disabled". Choose "Disabled". Click Apply or OK. SiliconDust will update the registry.
Now restart MC and run Manage Devices. That removed device will no longer show up.
So, for HDHomeRun tuners, in order to remove an unwanted device, you need to remove the physical device (unplug power, and unplug ethernet cable), AND run HDHomeRun Setup and disable the device from there.
The opposite is also true. If you want to put a good HDHomeRun device back online, you should plug and power cable, plug the network cable, AND run HDHomeRun Setup. The device will show up with Status "new". After click OK or Apply, the status will become "OK". Now MC will pick it up (restart MC if necessary).