Hello Steffen
I think what you have done is correct - placing each of the two maps on a separate canvas, and selecting "separate controls", then creating a single course that spans both maps.
When printing each of the two parts, you need to select the correct canvas for each part. So for part 1, select canvas 1, for example, and for part 2, select canvas 2. Condes is not smart enough to detect the correct canvas when multiple canvases are in play.
Could this be the culprit?
If the issue is more tricky, you are welcome to e-mail me a copy of the event file, and I'll take a closer look.
Regards,
Finn