I have exact same issue in multiple DAWs - Cubase 11, Reaper - Windows 10. I have tried multiple interfaces BOSS GT-001 and SSL 2+.
After playing around in Helix Native for some time, audio output suddenly stops. The only way to get it working is to unmount the plugin on track and reload which is annoying.
Same happens in Reaper. Though I see main output track as "Track Muted" when this happens in Reaper.
Can this be because switching from one preset to other sometimes suddenly cause a noise peak, causing the DAWs to mute the sound output to prevent ear damage.