Thank you Daid!
When printing a model with a single material yesterday one M302 command at the start of the Gcode did the job, so I got the feeling that it had something to do with the hotend change.
I started a small print of 15 layers in which i added M302 after each T0 and now I have extrusion on every layer with both extruders. So it works!
I just started a larger print of 378 layers, so we will see how it turns out.
Thanks again for the quick answer!