The least mind bending, for me anyway, would be for you to just delete all of the entries and just let it rebuild.
First, before deleting them all, you can go through Keychain, double click on a dupe entry, click the Show Password box in the lower left of the Info window that comes up to retrieve the Password and Account name. Write them down, then delete the entry from the Keychain list. This will make it easier to rebuild as you'll know what your account names and passwords are. If there are different passwords and account names for the dupe entries you'll have to figure out which one is the right one. After deleting the Keychain entries, if you're not sure which log-in info is correct, when rebuilding the keychain don't click the box that says Remember Password until you're sure.
Once you're sure of the right password, to get the dialog that comes up to enter the password again, you'll probably have to quit the app. I know Mail works like that. If you enter the password and tell it to not remember, it will still let you access the account until you quit the program, then the next time you try to access the account after quitting the program it will throw up the log-in window and you can then click Remember Password when you're sure you have the right log in info.
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