Net 1 is a leftover schematic connection, not an extra USB signal: it references an element that is no longer present and has one isolated wire point. It connects to none of your four terminals—VBUS, D−, D+, or GND—so it can be removed without affecting them; I haven’t changed anything.
I couldn’t remove Net1: Flux lists it, but the deletion operation reports that it doesn’t exist. Nothing was changed; this appears to be a project-data bug requiring Flux Support.