Onur
It is not possible to change flash configuration values using the in-circuit programming (actually it is but it would need the complete first sector to first be backed up in SRAM, modified accordingly and written back, which is risky since power loss during the process would cause program loss).
The method to use is to change it in the code.
If you use MCUXpresso's SDK it can be done by modifying the startup file called something like "startup_mke18f.c" at the following location:
//*****************************************************************************
// Flash Configuration block : 16-byte flash configuration field that stores
// default protection settings (loaded on reset) and security information that
// allows the MCU to restrict access to the Flash Memory module.
// Placed at address 0x400 by the linker script.
//*****************************************************************************
__attribute__ ((used,section(".FlashConfig"))) const struct {
unsigned int word1;
unsigned int word2;
unsigned int word3;
unsigned int word4;
} Flash_Config = {0xFFFFFFFF, 0xFFFFFFFF, 0xFFFFFFFF, 0xFFFF7DFE};
You need to work out what the bytes mean by studying the users manual and then adjusting the bits accordingly.
Or you can modify this to do it in a more maintainable and portable fashion by creating a struct and some meaningful defines (as the uTasker project has done since 2011).
Regards
Mark