Imports should usually be done on a fresh Blesta install. If there is a conflict between the user in Blesta and WHMCS, the import will result in an error. It's also important that your Staff user not be the same in WHMCS also. So yes, I would say remove the duplicates.
Also, backup your Blesta database prior to the import. If anything goes wrong, you can restore the database and be able to re-attempt.