Hello smitesh,
You are doing it the correct way. When you reprogrammed the chip to make your change, you also erase ALL the flash memory.
If you want to prevent your data from being erased, you will have to write protect that block of flash memory. The only way I have seen to do this is to use the Flash Progrmmer from TI and write protect that block of memory. You can search the forum, there may be a way to do it through code.
The SmartRF Flash Programer Guide can be found here: http://www.ti.com/lit/ug/swru069f/swru069f.pdf
Thanks,
