I just got word from printed solid that it's time to return the fried board so I'm going to wrap this up. Thanks you both for the time and attention. At least we learned that ground loops need to be taken seriously, and that U3 and D2 have certainly failed.

I just got word from printed solid that it's time to return the fried board so I'm going to wrap this up. Thanks you both for the time and attention. At least we learned that ground loops need to be taken seriously, and that U3 and D2 have certainly failed.

I like your theory, @bearer . I wanted to see what condition D13 was in but I can't seem to find it anywhere on my board. I will have to fire up kicad and search for it on the board layout to be sure of where it is.

VBUS on my PC is 4.6V (seems low but it's consistent across all my ports?) so that's probably fine. I only have to worry about ground loops now regarding that port.

I desoldered D2 and it is indeed a jumper now, not a diode.

With D2 out of the way, I'm no longer reading half an ohm of resistance between pad 12 of U3 and GND, and the duet 2 wifi seems to have kicked its smoking habit. R85 and R86 are both just 0.15Ohm so I'm guessing that heat was from 4.6V across 0.075Ohm through those two resistors. Yikes. It's possible that my finger tip was burned by R85 and R86, not D2.

@bearer You're right, the reverse voltage on that diode is 40V and maximum current is 3A.
Tomorrow I've got a few things to check.
Vbus of the computer I connected to, though it hasn't cause me problems with any other devices in 5 years.
Current running through the USB port. It should be limited to 500mA.
I will see if I can't also get the voltage across D2, R85, and R86.
And I will check for continuity between pin 8 of the U3 pads and any other nets that it's not supposed to.

Thanks for your input. I'm getting the impression the Duet community is pretty robust.

sources
https://raw.githubusercontent.com/Duet3D/Duet-2-Hardware/master/Duet2/Duet2v1.04/Duet2_1.04c_Schematic.pdf
https://www.mouser.com/datasheet/2/315/DB2W40300L_E-1141713.pdf

I don't know if any of the engineers read these posts, but the curiosity was getting to me. I plugged the board in again to a micro usb breakout with a current limited power supply with nothing else plugged in to see what components were heating exactly. D2 seems to be passing a lot of current. Even after using hot air to desolder U3, D2 was still heating up enough to give me a little diode shaped burn on my finger after only a few seconds.

U3 seems to be the victim of some other failure mode rather than with the chip itself. If there's any particular points any of the developers would like me to probe, let me know.

@Phaedrux Thank you. I've already filled out the reseller warranty form through Printed Solid. I will update the link in the form to point to your post instead of the general thread.

Yes the board was powered by 24V VIN when I connected to the PC.

To add context.

I was replacing the CR-10S Pro V2's control board.
Endstops, Stepper motors, BL touch, thermistors, and power wiring for the board and bed was connected and the 24V power supply was on. Heater cartridge power for the hotend was left disconnected. I did not notice any issues while this was the case. I wish I could recall which LEDs were lit on the board, but the always-on fan was spinning well and sounded normal. VFAN is jumpered to VIN, which should be 24V based on the 24V Meanwell power supply. I have not checked the power supply with a multi-meter yet.

After I was satisfied that nothing blew up yet, I wanted to flash the latest firmware to the board. I connected the printer to my PC and the diag LED next to the micro USB port flashed red for an instant before I heard a snap and smelled smoke. I immediately removed the cable and inspected the board. That's when I noticed the U3 chip stood out to me with a circular burn near the corner.

BL Touch was connected as shown here https://d17kynu4zpq5hy.cloudfront.net/igi/duet3d/KUDxTZSs3rnd3JVH.full
Hopes this context helps determine the cause of these U3 failures.

The duet 2 wifi I received as part of order my Printed Solid order, PS-139302 from June 1st 2020 has suffered a failure of the A4403 buck converter chip on the first time I connected it to my pc. It shows a burn mark in the same spot as other threads on this forum. The duet 2 wifi has been sitting in storage unused until today.

Serial Number: 1219.1646
VIN of 24V

Tried plugging the board into my pc a second time and I could feel the area of the board under U3 heating up rapidly. No further troubleshooting taken.

Thank you for your time.