The program you want is called iMPACT and it is part of the WebPack ISE 14.7 package (free).
If you search Google you may find a way to install iMPACT without installing the entire ISE.
I don't know anything about serial numbers. I don't even know how you would find it buried in tons of startup code. In fact, you may not even be able to read the contents of the configuration EEPROM. It's been known to happen that this stuff is all encrypted. It depends on the logic family. Personally, I don't think there will be a positive outcome.