At the Moment yes, I just Installed Arducopter 3.5.5 with Missionplanner again to give it another try. I dont know which Ground Station and which flight stack I am gonna use finally . I would prefer to Work with Missionplanner because of better documentation and nice Support at the Forum :-).
I did the reinstallation of the FW for the Flow Sensor with QGC.
And before I tried PX4 with QGC to see if the Flow Sensor would work with this workchain. But finally I reinstalled APM with Mission Planner again.
Right now the System reconized the flow sensor. Will see if it does it again.
EDIT: I think right now it is a matter of if I am plugging the USB in while it is booting up or not.
Thank you!