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main app not starting from within bootloader

My goal was to make a bootloader, that, when not requested, still goes do DFU mode for 5 seconds,

so that there is always an option to get to the bootloader after boot, even when the application is too broken to request it.

My issue is that in my main app, the softdevice somehow fails to initialize, if the app was started from the bootloader after SD initialization in the bootloader.

I assume that the issue might be an already initialized softdevice by the bootloader.

So, is there any chance I can boot into the application from the bootloader after already enabling everthing BLE-relevant in the bootloader?

Here is my modified nrf_dfu.c:

/**
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 * 
 * All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without modification,
 * are permitted provided that the following conditions are met:
 * 
 * 1. Redistributions of source code must retain the above copyright notice, this
 *    list of conditions and the following disclaimer.
 * 
 * 2. Redistributions in binary form, except as embedded into a Nordic
 *    Semiconductor ASA integrated circuit in a product or a software update for
 *    such product, must reproduce the above copyright notice, this list of
 *    conditions and the following disclaimer in the documentation and/or other
 *    materials provided with the distribution.
 * 
 * 3. Neither the name of Nordic Semiconductor ASA nor the names of its
 *    contributors may be used to endorse or promote products derived from this
 *    software without specific prior written permission.
 * 
 * 4. This software, with or without modification, must only be used with a
 *    Nordic Semiconductor ASA integrated circuit.
 * 
 * 5. Any software provided in binary form under this license must not be reverse
 *    engineered, decompiled, modified and/or disassembled.
 * 
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 * OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
 * OF MERCHANTABILITY, NONINFRINGEMENT, AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL NORDIC SEMICONDUCTOR ASA OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
 * GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
 * HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
 * LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
 * OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 * 
 */

#include "nrf_dfu.h"
#include "nrf_dfu_transport.h"
#include "nrf_dfu_utils.h"
#include "nrf_bootloader_app_start.h"
#include "nrf_dfu_settings.h"
#include "nrf_gpio.h"
#include "app_scheduler.h"
#include "app_timer_appsh.h"
#include "nrf_log.h"
#include "boards.h"
#include "nrf_bootloader_info.h"
#include "nrf_dfu_req_handler.h"

#define SCHED_MAX_EVENT_DATA_SIZE       MAX(APP_TIMER_SCHED_EVT_SIZE, 0)                        /**< Maximum size of scheduler events. */

#define SCHED_QUEUE_SIZE                20                                                      /**< Maximum number of events in the scheduler queue. */

#define APP_TIMER_PRESCALER             0                                                       /**< Value of the RTC1 PRESCALER register. */
#define APP_TIMER_OP_QUEUE_SIZE         4                                                       /**< Size of timer operation queues. */


#define APPLICATION_START_TIMEOUT      APP_TIMER_TICKS(5000, APP_TIMER_PRESCALER)
APP_TIMER_DEF(application_start_timer);

// Weak function implementation

/** @brief Weak implemenation of nrf_dfu_check_enter.
 *
 * @note    This function must be overridden to enable entering DFU mode at will.
 *          Default behaviour is to enter DFU when BOOTLOADER_BUTTON is pressed.
 */
__WEAK bool nrf_dfu_enter_check(void)
{
    /*
    if (nrf_gpio_pin_read(BOOTLOADER_BUTTON) == 0)
    {
        return true;
    }
    */

   

    if (s_dfu_settings.enter_buttonless_dfu == 1)
    {
        s_dfu_settings.enter_buttonless_dfu = 0;
        APP_ERROR_CHECK(nrf_dfu_settings_write(NULL));
        return true;
    }
    return false;
}

void application_start_timer_handler(void * context){
    NRF_LOG_INFO("application start timeout\n");
    if (nrf_dfu_app_is_valid())
    {
        NRF_LOG_INFO("Jumping to: 0x%08x\r\n", MAIN_APPLICATION_START_ADDR);
        nrf_bootloader_app_start(MAIN_APPLICATION_START_ADDR);
    }else{
        NRF_LOG_ERROR("no valid app\n");
    }
}


// Internal Functions

/**@brief Function for initializing the timer handler module (app_timer).
 */
static void timers_init(void)
{
    // Initialize timer module, making it use the scheduler.
    APP_TIMER_APPSH_INIT(APP_TIMER_PRESCALER, APP_TIMER_OP_QUEUE_SIZE, true);

    app_timer_create(
        &application_start_timer,
        APP_TIMER_MODE_SINGLE_SHOT,
        application_start_timer_handler
    );
}


/** @brief Function for event scheduler initialization.
 */
static void scheduler_init(void)
{
    APP_SCHED_INIT(SCHED_MAX_EVENT_DATA_SIZE, SCHED_QUEUE_SIZE);
}


static void wait_for_event()
{
    // Transport is waiting for event?
    while(true)
    {
        // Can't be emptied like this because of lack of static variables
        app_sched_execute();
    }
}


void nrf_dfu_wait()
{
    app_sched_execute();
}


uint32_t nrf_dfu_init()
{
    uint32_t ret_val = NRF_SUCCESS;
    uint32_t enter_bootloader_mode = 0;

    NRF_LOG_INFO("In real nrf_dfu_init\r\n");

    nrf_dfu_settings_init();

    // Continue ongoing DFU operations
    // Note that this part does not rely on SoftDevice interaction
    ret_val = nrf_dfu_continue(&enter_bootloader_mode);
    if(ret_val != NRF_SUCCESS)
    {
        NRF_LOG_INFO("Could not continue DFU operation: 0x%08x\r\n");
        enter_bootloader_mode = 1;
    }

    // Check if there is a reason to enter DFU mode
    // besides the effect of the continuation
    if (nrf_dfu_enter_check())
    {
        NRF_LOG_INFO("Application sent bootloader request\n");
        enter_bootloader_mode = 1;
    }

    bool start_application_timer = enter_bootloader_mode == 0;

    enter_bootloader_mode = 1;

    if(enter_bootloader_mode != 0 || !nrf_dfu_app_is_valid())
    {
        timers_init();
        scheduler_init();

        // Initializing transports
        ret_val = nrf_dfu_transports_init();
        if (ret_val != NRF_SUCCESS)
        {
            NRF_LOG_INFO("Could not initalize DFU transport: 0x%08x\r\n");
            return ret_val;
        }

        (void)nrf_dfu_req_handler_init();

        if(start_application_timer){
            NRF_LOG_INFO("starting bootloader timeout\n");
            app_timer_start(
                application_start_timer,
                APPLICATION_START_TIMEOUT,
                NULL
            );
        }

        // This function will never return
        NRF_LOG_INFO("Waiting for events\r\n");
        wait_for_event();
        NRF_LOG_INFO("After waiting for events\r\n");
    }

    if (nrf_dfu_app_is_valid())
    {
        NRF_LOG_INFO("Jumping to: 0x%08x\r\n", MAIN_APPLICATION_START_ADDR);
        nrf_bootloader_app_start(MAIN_APPLICATION_START_ADDR);
    }

    // Should not be reached!
    NRF_LOG_INFO("After real nrf_dfu_init\r\n");
    return NRF_SUCCESS;
}

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