This workflow is not what i would do. How is routed audio?
I would do something like this:
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SooperLooper in the Main Bus. MIDI-learn sooperlooper controls using absolute MIDI learn (controller/learn options submenu), so you can control it regardless of the selected chain. Should we force absolute MIDI learn on Main Bus, @riban?
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Chain with ZynAddSubFX: channel 1
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Chain with LinuxSampler: channel 2
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etc.
If you want to layer sounds, then use the same MIDI channel for them and enable “Active MIDI channel” from admin menu.
If you use a single keyboard for playing, set ACTI mode for it. Then learn your ZS3s.
Regards,