Good point.
I guess the most important thing is to match your names and SSNs on W-2s (and 1099, 1098, etc) with those on 1040. Unless you triggered an audit, the IRS offices probably won't take the trouble to check up your previois files and compare your names.
As to my son's case, we simply replaced his ITIN with the SSN in 2006, and no questions asked.