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BL652 Default pull up state

We are using Lairds BL652 module in our product and develop code for it using the Nordic Semiconductor nRF5 SDK and flash it using jlink. Referring to the attached schematic, we use SIO_16 to turn on power to a boost converter and SIO_14 to drive the mosfet using PWM. However, since the BL652 by default has these pins configured as an input with a pull up, it causes a problem when we need to flash firmware for the first time or turn on the board with the pre-loaded firmware. Due to the default pull up state, the mosfets turn on and essentially short the supply through the inductor.

Is there a way to turn off the default pull ups before flashing the module with custom firmware. It wasn't clear if this is possible by configuring the nAutoRun and SIO_02 pins.

The method we currently follow is to force SIO_16 Low using a jumper JP2. The module is then erased, after which the jumper is removed and the mode is reflashed with the desired firmware. This feels a tedious process.

The other method contemplated is to replace R3 with a 2K Ohm resistance so that the gate voltage of Q2 falls below 0.3 x VDD, where VDD is 3.3V.

I'd like to know if there is a better alternative?

I've asked Laird the same question, but am hoping someone could answer here too. 

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