Did you try to open up Microsoft Outlook and look in contacts to see if they were there. Or check the deleted section in Outlook to make sure activesync didnt stick them there. I had this problem the first time I flashed my new rom. Activesync syncs your contacts to outlooks contacts. and then sometimes when you re-sync your device again with the new rom it looks at ur current contacts on your device (which should be empty) and then assumes to do the same to your contacts in Outlook so itll stick all of your previously saved contacts in the deleted section.
If they are there, just select all, and drag them back into contacts and then re-sync your device. Hope this helps!
Also if you use gmail or yahoo, sync all your contacts to your address book there, just in case.
