I see you have a dust shoe, are you using it? Is the vacuum tube grounded? If yes, is it connected to the Shapeoko frame to provide a channel for static discharge? Have you moved your computer and/or moved the USB cable, a small movement of the USB connector can also create a drop in communication. That port can be very sensitive.
Not sure if you are asking me about the dust shoe or not. But, yes I have been using the dust shoe with a full dust collection system (1500 scfm) it isn’t fully grounded to the ShapeOko, but I was having disconnect issues even if it wasn’t being used. Grounding everything the way I did, instead of spending time trying to find the exact culprit of the disconnect (had to finish a captain America shield for a bday present, hence the frustration) has given me a couple of months of no disconnect problems so far.
Unfortunately, it seems like these disconnect may come from several sources and are a bit random so it is hard to pinpoint the exact source so you need to cover all bases. Maybe you have most things covered but you need to add shielding and grounding to the dust collection system. The other day, the wire between the vacuum to the Z plate somehow disconnected. When I removed the tube, I was zapped from the static in the tube, it did not have any place to evacuate until I touched the vacuum tube. If this found its way to the controller, USB cable or computer, it could have caused a disconnect or worse.
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