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A file or library saved before "modes" was an override group has a mode chosen on a layer inside an instance without its marker, so the next rebuild or library import still put the main's mode back. Copies follow their main layer's modes when the main changes them, so a layer inside an instance on other modes chose them itself. mark_layer_modes marks those when a file opens and when a published library is read from a file or a server. Layers on their main's modes and top-level instances stay unmarked.