SmartConnect has an update existing option, but not an update only option, but this doesn’t mean it is impossible to update only. SmartConnect has a Multi Data source type under Bulk Data Load. Multi Data allows you to join queries from different data sources and combine them into a virtual staging table to be used for an import.
In my example, I am sending GP Customers to CRM Accounts. I don’t want to create new CRM Accounts so I will use Multi Data Source we can include our Source data from GP, and destination data from CRM. I will join the two sources on the Customer Number. I use an inner join so only records that exist in CRM are returned.