Please see Section 7 in the S110 SoftDevice Specification 2.0 for more information regarding accessing flash when the SoftDevice is enabled.
When the SoftDevice is enabled you can either use:
sd_flash_write() If the flash operation is succesful you will get a NRF_EVT_FLASH_OPERATION_SUCCESS event in sys_evt_dispatch(). I recommend you to have a flag that is set you do a flash operation, and is unset when you get NRF_EVT_FLASH_OPERATION_SUCCESS. Check the flag before you do a flash operation.
Pstorage, which is a module for handling flash operations. This is what we use in our BLE examples. There is also alot of information found on this forum.
