Borders being shut has nothing to do with consular processing. Borders are open for work purposes and probably she was trying to say consulates being closed.
If your company never processed H1 with consular processing they would be nervous with everything shut down now.
btw...how long have you been commuting? And your HR probably overlooked the commuter thing. Did you ever tell your HR about commuting? If yes, they should have filed it right up front, someone just slacked here and messing up lives..!!