If you haven't got a response about preserving DD+ from HDDVD movies, this is what I do.
I run Clown_BD as usual, keeping TrueHD if there, but if it isn't, I select Core. Let it run. After it is finished, I then use HdBrStreamExtractor (h**p://stuff.griffore.com/stuff/HdBrStreamExtractor.zip
) which is a GUI for eac3to so it must be unzipped to the same folder as eac3to (just use the eac3to that comes with Clown_BD). Select the Input, click on Feature(s), once it shows the main movie, click on it and then it will scan through the movie and show you the available streams. Once the DD+ track is shown, select it and from the Extract As drop-down menu, select eac3. Add an output destination and then select Extract.
Once it is complete, run tsMuxeRGUI.exe (which can be downloaded from: [h**p://www.videohelp.com/download/tsMuxeR_1.10.6.zip
- extract tsMuxeRGUI.exe to the same folder as tsMuxeR in Clown_BD). Click on Add, navigate to the folder where your Bluray file was saved to from Clown_BD, double click it, double click BDMV, double click PLAYLIST, select 00000.mpls and click on Open. Navigate to where you DD+ file is and drag and drop it to the Input Files window of tsMuxeR. In the Tracks section, keep the TrueHD selected (if applicable), uncheck the Core audio (should be 640kbps DD) saved from the first run of Clown_BD (once again, if applicable), highlight the DD+ track by clicking on it once. In the General Track option drop down, select eng. For output, select Blu-ray disk, browse to a new save location and click on Start muxing.
In 8 to 13 minutes or so, you should have a new bluray movie with the DD+ track added. One note, some movie files will be too big to fit on a BD-R 25 GB disc if you have both TrueHD and DD+ as audio options. I hope this message helps and it's a little clearer than mud.