the mutes can be triggered by going into mixer menu and then pressing a track button (or drum instrument button for drum mutes) without holding any other button.
mutes are really stored in flash with the patterns. this has been a deliberate choice so you can arrange with mutes. when you say “when the pattern loops”, are you in pattern chain mode? then it´s correct, because the pattern chain recalls the pattern from flash, also recalling mutes.
we considered high and low to add another set of non-flash “live” mutes, but that would have complicated the topic even further. and then we realized that usually there is mostly another set of “live” mutes in the sound generators that are being triggered by the Zaquencer anyway (mixing board or volume knobs).