If u went for a 12 wk u/s and it showed the measurements of a 9 wk old fetus, is this enough of a difference to change the due date?

Yes: A 9 week sonogram is accurate within about 5 days. In your case your sonogram would be used to calculate your due date.

Yes! Yes! Yes!: You were not 12 wks when you thought you were! you were 9 weeks (as long as the 9 week fetus showed fetal heart activity). The only way you could have a 9 week size fetus and really be 12 weeks would be if the fetus had died at 9 weeks and been retained in your uterus. End of story.