same issue with my android/windows account
if i mute channels & turn on "Hide muted channels" and "Hide muted channels by default" (in fluxer://settings/user?tab=advanced_settings§ion=advanced-settings-chat) the channel disapear if i click "mark as read" but if there are new messages them apear back in my channel list.
turn on/off "Hide muted channels by default" dont fixed this problem.
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Comment by Patrix