The bootloader is only doing its thing for a few seconds, when resetting or loading a new sketch.You could ignore it completely and make those changes in the pins_arduino.h header file and that will (should) handle things while your sketch is running.It's in the hardware/arduino/variants/leonardo folder.Then (I am pretty sure) you'll see the TX and RX leds working 'inverted' only when the bootloader is running, but the rest of the time they will work as intended.Cheers!
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