That would depend on the data you are getting back. Does it include a value in one column that uniquely identifies that contact and which matches to a value in your database that uniquely identifies the same contact?
If so, Import Records has an Update Matching Records in Found set option that you can use to update your existing records with the new data, but since obsolete data cleaned from your import file will still be present in your database, this will only partially update your data.
It may be simpler to delete all records from your contacts database and then import--but look out for cascading deletes of related records that you don't want to take place. You may find that you have to save a clone of your database file, import the cleaned data and then import data in other tables from your current database file. Even then, you may want to find and delete records in related tables that no longer link to a contact record because it was deleted from your list of contacts.
Thanks for the reply. Looks like reuploading the data into a new file will be the best option.
I'll add in a field that can uniquely identify each record, so hopefully this process can be easier next time.