How are duplicates handled in a contact import automations?

We have an automated contact import set up to run daily. It works, but it doesn't detect duplicate entries - if a contact already exists, rather than update the contact information, a new record is then created for that same person. We are using a unique ID (student ID) for each individual so it should be easy to detect duplicates, but I don't see any way to specify this in the automation. This functionality is different from when a list of contacts is uploaded manually to a directory - in that case, records for the same individual get updated rather than creating new records.
Is there a way to have the automation deal with duplicates correctly? By creating multiple records for the same unique ID, the authentication we have set up for one of our surveys doesn't work for people who have more than one record.