Are they Google contacts? If what's on your sd is exactly correct, you may want to remove contacts in Gmail on a computer first. However, gmail on a computer has a "merge duplicates" function too.
Basically, go into "accounts and sync" and turn off all sync.
Then go into application manager, open "contacts storage" and do a "clear data".
Then you can import and sync to your heart's content.
Worth noting though if your Gmail contacts are a mess, not addressing this will mean when you turn sync on, you will sync the mess back