Issue with UART Disappearing When Using I2C on BeagleBone AI-64

General Discussion
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I would check what I2C peripheral bone_i2c_2 is actually using.
P9.17 and P9.18 uses I2C6 and only potential conflicts with UART3 TX pin depending on how it is muxed.

I created a spreadsheet with all pin muxs for the AI-64 here pinmux spreadsheet