Patching a HEX file would be pretty easy in some high level language like Ruby or Perl, but a little annoying because HEX is actually a little complicated. It has checksums, etc. It would probably be a lot easier to set the db where the serial number is supposed to live to some distinctive value. Then compile to some more raw format (maybe they call that bin). It will be easy to see what to patch, then. Just modify the two bytes or whatever, taking into account endianness issues. Then convert the bin to a HEX or whatever is required.

If you do it that way, you can write the simplest possible program. It will just need to modify a few bytes at a certain offset into the object file.