Please save the settings, save the project, and ensure that the named setup is selected in Docuflow. 

Just to be clear, it is nothing to do with Docuflow, as it is Revit that handles the export natively, with its own native settings.

You can export using the same setup directly in Revit and compare the results.

Export views on sheets and links as external references: Clear this check box if you want any Revit or DWG links in the project to be exported to a single file rather than to several files that reference each other.

Even if you clear this box, the program still continues to export external links.

The options related with the DWG file export are nativelly the ones from Revit. Docuflow uses therefore a setup that is created and changed using the Revit DWG options dialog described here.

https://knowledge.autodesk.com/support/revit-products/learn-explore/caas/CloudHelp/cloudhelp/2018/ENU/Revit-DocumentPresent/files/GUID-E8443B4B-D55B-4630-BEE3-D2D8628CA17B-htm.html

Once saved that setup will have a name, and can be selected inside Docuflow.

Among those options one can select what version of DWG one wants to export or if the DWG shall export all views as separate DWG or merged into a single file.

In the General tab one can control the last:

Export views on sheets and links as external references: Clear this check box if you want any Revit or DWG links in the project to be exported to a single file rather than to several files that reference each other.