I managed to export wowza recorded DVR chunks to one mp4 file using the following method :
Install on you local computer or on your server the following script :
Download all chunks, based on manifest file, using the command :
more information here : https://github.com/K-S-V/Scripts/wiki
php AdobeHDS.php --manifest "<url to your DVR manifest file>/manifest.f4m?DVR" --delete
This will produce a single mp4 file ( in flv container ).
Download the generated flv file and change flv container to mp4 using MP4tools.
Use the "MP4" tab and configure "passthrough" for video and audio track.
You can extract a specific segment of your video if needed with the same tool using the "Edit files" tab
The resulting file is proper mp4 file.