This is not true. If Omega does the replacement, they would no doubt have the case engraved with the serial number on the movement, and the old case would be kept by Omega, because clearly they do not want 2 cases out there with the same serial number.
As a certified Omega watchmaker, if I wanted to order in a case, I can do this two ways. I can simply order a case, and it will not have a serial number on it. Or I can send the old case back to Omega and request that they send me a replacement with the serial number engraved on it, but again the old case remains with Omega.
So if the case was changed, it likely wasn't done by Omega, or by someone who cared enough to follow the procedure to get the case replaced properly, and the OP is sort of paying the price for that now. There are also fake Speedmaster cases and parts out there, but for now I would assume that whoever looked at this and declared it genuine actually knew what they were talking about.
Cheers, Al
