In order to remove ALL Bongo data from a file, you have to do the following:

1. Type in -SaveAs on the command line.
2. When prompt:
   Save file name <C:\Users\Usernamehere\Models\Examplefile.3dm> ( Version=5  SaveSmall=No  GeometryOnly=No  SaveTextures=No  SavePlugInData=Yes  Browse )
   Set  SavePlugInData=No
3. Press enter

Please note! When no plug-in data is saved, this means that NO plug-in data at ALL is saved. The command will strip the file from all plug-in data. So you will also for example lose your rendering settings and so on.