Your right. This is a Saleforce issue but You can actually deal with it in the Connector.
To the Salesforce API you can send the parameter ”ALL ROWS" to fetch all rows. That parameter is what QueryAll sends to the API from the Connector.
I didn't know about this auto-archive function i Salesforce until just the other Day. Our Salesforce consultant knew about it and the parameter. He also told that the function by default archives records older than one Year but that You can change that somewhere in the Settings. We have older than 3 Years.