Hello Axel,
Based on looking back through our email correspondence, am I correct understanding that you're referring to:
1. Using the stop switches on your Ahlborn Hymnus III digital organ with Hauptwerk, and:
2. The problem you're having arises when you try to trigger one of Hauptwerk's virtual combination pistons using one of your digital organ's physical pistons?
If so, as covered in the 'Playing Hauptwerk live from a digital organ' section of the main Hauptwerk user guide (pages 179-180 in the current v4.2.1 version), it can never reliably be possible to use both a digital organ's stops with Hauptwerk, whilst also using the digital organ's combination pistons to trigger Hauptwerk's combination system, since the digital organ's built-in combination system will inevitably 'fight with' Hauptwerk's combination system over the states of the stops. (The only exception might be if you were able to disable the digital organ's internal combination system completely, but I know of no digital organs that have an option for that.)
Hence you have to choose either to:
A. Use the digital organ's stop switches with Hauptwerk (in which case you mustn't auto-detect its combination pistons to Hauptwerk's virtual pistons/buttons), or:
B. Use the digital organ's pistons to control Hauptwerk's combination system (in which case you mustn't auto-detect its stops switches to Hauptwerk's virtual stops).
In that way you will only be using one combination system (the digital organ's combination system in the case of option A, or Hauptwerk's combination system in the case of option B). In my experience most people prefer B (since the selection of stops switches on any given model of digital organ are unlikely to match exactly with multiple different sample sets).