I’ve been doing this quite a bit myself, and haven’t found any issues
that you would not find in a bare metal (non RTOS) application - so
really FreeRTOS doesn’t add any complexity. As per a non RTOS
application you need to jump to the start up code of the application
being booted, so it initialises its variables etc, (not jump to main()
of the application being booted), set up the vector table base address
(so the vector table of the application is used, not the vector table of
the bootloader), etc, etc.
In addition to disabling interrupts of any peripherals that were enabled
by the bootloader you will also need to somehow disable the systick
interrupt - but for a belt and braces approach I tend to globally
disable interrupts too before jumping to the application (“cpsid i”).