Okay, let's try to understand the differences, shall we? (if anyone wants to see the files, shoot us a message or write in thread)
Of the ~115 bytes of difference, almost all of it are hashes, belonging to the IVFC hashtree. Only a very small part (~16 byte?) is actual changed data. Interesting offsets are 0x00C050, 0x010B050 and (possibly) 0x10B30F. Now if you compare 0x00C050 in b4 with 0x010B050 in aftr, that data is identical. Savegames actually have two partitions, one of which is the backup partition. I assume b4 is without, aftr with the update nag. 0x00C050 then belongs to the active partition, 0x010B050 is the backup partition. The true interesting data starts at 0xC058 - this is all zeroes in b4, and contains one 32 bit value in aftr (not the only change, but a good starting point).
Now, you can't just take the data over, because all those pesky hashes have to be accounted for, too. We will find a way to handle this, though.
EDIT: What we need is a savegame editor - is there something like this?