BI Connector is now a certified connector for Power BI. As part of the certification some changes were introduced to its working model and the interfaces. This change caused the existing Power BI workbooks (created using BI Connector version 3.8 or lower) to fail after the BI Connector was upgraded to the Power BI certified version 3.9 and later.
At this time the only way to get the existing Power BI workbooks to work properly with a certified version of the BI Connector is to manually make the following modifications to the workbook configuration.
Open your existing Power BI workbook.
Click on “Edit Queries” icon from the Home menu.
In the Power Query Editor, select each table that you have loaded and click on the “Advanced Editor” icon from the Home menu. 
You’ll see something similar to the below Power Query.
Change the "Source" in first line to “BIConnector.Contents("<your DSN name>")” and click on “Done”.
Do this for all the tables once it is loaded successfully.
Now you can open the older version of Power BI workbooks with the upgraded certified BI Connector within the Power BI Desktop.