Hi.
All these settings that you are mentioned are stored as a default in area 0x400 – 0x410 in memory area and are very nicely described in reference manual.
- Securing option:
There are some securing options that allow you protect content of Flash in final products against to steal it. By these options you can secure Flash also against mass erase and this is the worst case for you, because if you forgot setup backdoor key you are not able to unlock device and then you can get rid of the MCU (But this is right combination for final product distribution).
In case that you want to secure the chip and keep still full control on writing into the flash, so you just enable secure options and keep unprotected area of flash that you want to write run time.
If you are used "Processor Expert", you can change "Flash security" option to "Disable":
I believe that these hints help you.