Go to your original workbook that has the dashboards in it. Open up a NEW data source and connect to the Prep-created datasource you published on Server.
You will now have 2 separate data sources in your workbook, one for the old extract and one for the new published data source.
Right-click on either of the data sources and select "Replace data source" from the popup menu. Replace Data Sources - Tableau
You'll have to recreate the folders you've created but otherwise everything should map over correctly. Then you can close the OLD data source and your workbook will use the new one.
PS: you cannot connect Prep to a twbx file.
There are some caveats to using Replace Data Source, it's not guaranteed to replace *everything* the way we want... aliases, color settings, nested calculated fields, and some other bits can get lost in the Replace Data Source, so you'll need to carefully review each view to make sure it's working. See https://community.tableau.com/ideas/1954 for a long-standing feature request around this.