Even the Raspberry Pi Foundation used GPIO numbers over (congruous) physical pin numbers: https://www.raspberrypi.org/learning/introduction-to-processing/worksheet-2/ Switch our examples as well, so that it they're more clear and hardware-agnostic.
It appears as if using the I2C pins for GPIO requires a restart of the Raspberry Pi before the I2C interface can be used again. Play safe and move the examples to pins that aren't used for anything else.
