To be clear, I definitely recommend clean installs. MUCH safer... HOWEVER, a clean install doesn't have to involve a format. The Windows Vista/7/2008/2008R2 installer, if it cannot do an upgrade does a clean install. It does this by putting aside the old install in a separate folder. If you cheat and do something silly like copy the old program files folder back and wipe out the correct program files folder, I wouldn't be surprised to see errors.
My interpretation was that that JPMCNYC had 2008 x86, put the x64 CD in the system and the system did the clean install by shifting over the old install. So no upgrade in my actual definition of upgrade was done. It was really a migration, since there would have been some hacking going on to get it to upgrade (no idea what kind of hacking as I've never seen or heard of anyone "tricking" windows x64 setup into even attempting an upgrade of x86).
To me, since the only issue is with low disk space, I don't see why anything is "wrong" per se - other than there's an old install of Windows that can be (re)moved.
