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MCU reading wrong status of GPIO pin

Hi, I am trying to use P0.9(nfc pin) as gpio(input) to read the charging status of a battery from battery charger IC(BQ 24230). the Open-Drain Charging Status Indication of a pin is connected to P0.9 and Open-drain Power Good Status Indication of a pin is connected to P0.19 of MCU

We have also defined "CONFIG_NFCT_PINS_AS_GPIOS" in preprocessor settings.

Whenever I am reading the Charging status in simple (default Project NAME)UART code the MCU is able to read the correct status of pin but when I am doing same in (default Project NAME)DFU code I am not getting the correct values . can someone please help what additional settings do i need to do?

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