Just as every record in Workfront has a unique system-generated ID, so to does every record in Salesforce. I'd find some field on the Document object in Workfront to store the unique document ID from Salesforce. I'd try extRefID myself so it's something hidden from users.
Once you have that, you have something to compare against in your Fusion logic. 'Does this unique ID from Salesforce have a corresponding Document in this Project in Workfront? If no, download. If yes, ignore.'
If they're doing versioning on your SF documents, that will take some extra thought there.