FreeRTOS uses RTC1, app_timer.c also uses RTC1. So both of them cannot work together as it is.
There are two options to choose from when using FreeRTOS
Instead of using app_timer.c, you use app_timer_freertos.c. In this file instead of using RTC1 it uses RTOS timers API and freeRTOS is free to use RTC1 as no conflict exists.
This will only work in nRF52. Use change_freeRTOS_to_use_rtc2_instead_of_rtc1.patch which will force FreeRTOS to use RTC2. Now you can use app_timer.c (using RTC1) combined with FreeRTOS (using RTC2 after the patch)
