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I attempted upgrading my Ender 3 firmware to Marlin 1.1.9, and due to inability to find the directions about the Sanguino variant pin layout file, stupidly built with the "standard" (Arduino) file. Various stuff didn't work, and I figured out my mistake and rebuilt, but the extruder motor does not respond even after flashing back to the original firmware.

Did I destroy the stepper driver with incorrect pin mapping? (Aside: if so, why just the extruder and not the others?) Is this fixable or should I just order a new motherboard?

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About 15 minutes after posting this, it started working again. Either the driver had badly overheated and recovered after cooling down, or was never messed up and the firmware was just refusing to operate it with the nozzle cold. For the latter possibility, the stock firmware never had that behavior before, but maybe it's possible that some saved configuration to ignore nozzle-cold got lost in the flashing?

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