About all you can do is check to make sure the connections are good. You have have wiring from the front ports to the MB header. Remove the connectors and plug them back in. Make sure the pins in the connectors are fully seated as well. Pulled pins are notorious for causing connection failures. I have had USB ports go bad and I suspect due to static discharge. When this happened to me, however, the ports didn't disappear but showed as having a problem. Good luck.
I have two USB ports on the front of a PC that I use for backups. For no apparent reason they stopped working today. I plugged my printer into the ports to verify if they work and they did work with the printer. When I try to do a backup I get a message saying the port/drive does not exist. I went into the device manager and those two USB ports don't show there either. HELP...does anyone have any thoughts on what to do next?

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