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I encountered a similar issue earlier, and my solution was either to exclusively use D-shot outputs from the IOMCU or have the MAINMCU handle all D-shot outputs. I frequently ran into error code 0x1000 back then.
The interface resources tested for Ardupilot hardware controllers – 16 D-SHOT ports, and 2 CAN buses – are ample to cater to consumer-grade drones, vehicles, boats, and even underwater vehicles. If ever faced with insufficient connectivity, expansion would likely rely on CAN interfaces as a modular solution.
With a CUAV 6X with Pixhawk6X-bdshot firmware, with 6 blheli32 ESCs connected on a hexacopter (4 ESCs on main, 2 on aux) I get a reproducible internal error 0x1000 for IOMCU reset after arming. The copter still flies fine, but we need to find the cause of this.
Logs here:
https://drive.google.com/drive/folders/1fveumuzs7zw7zCqw7jKLHqiaXxx3k5nC?usp=drive_link
ping @andyp1per
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