Hello Mediator,
i've testet your tip and it is the missing link
Now i can batch remux my nero mp4 container / files to standard compliant mp4 with AC3.
After that i'am able to convert the new MP4 files to mk4 containers by using xmedia recode (the nero versions are not recognized to contain audio).
Then i can set up a job list with the new mp4 container as source for audio and video and select as target container mkv and choose copy audio and video.
Solved! thank you very much!