Hi Lakesh,
Did you ever find a solution for this? Probably the quickest solution is to figure out where the config data resides and write to the regions around it using a layout file.
It's an interesting problem that I suspect we'll see more often in the future, not just with UEFI. Storage of config data on the firmware ROM is becoming more common, and the firmware update utility of choice needs to become more aware of what portions of the ROM are safe to overwrite.
For ChromeOS platforms, we added a blob that maps the ROM content (flashmap, or fmap for short) so that our update scripts know which regions of the ROM to target when updating.
I'm not sure what the best way to do this for other systems, though. AFAIK this is all vendor-specific.