Can application modify/disable bootloader if started by bootloader

We have a partner that has developed a custom bootloader. They have enabled the watchdog in the bootloader. The bootloader transfers control to the application if the GPIO state it is looking for is not met.

Will our application be able to modify the watchdog after it has been started? My understanding is that the bootloader configuration is locked after it has been started, and only a reset other than a soft reset will clear it's configuration.

Or will we need to work with our partner to modify the bootloader configuration/interval so it's compatible with our application requirements.

We are using the nRF5 SDK.

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