I had this same Problem. I fixed it by disconnecting the battery. Reboot!
(disconnect the ground cable, look in your manual for proper disconnection. It’s different is you have autostop or not).
My usb worked for 4 months then one day it wouldn’t see the device. Tried all the usual stuff, different usb port/device etc. My phone would still connect so I knew the usb ports were working they just wouldn’t read the thumb drivess.
So I decided to try rebooting the system like I do with any computer when it’s not acting right. In the manual it says if you are going to flat tow the truck to disconnect the battery. (only 4×4 with 2 speed transfer case can be flat towed). So I disconnected the battery, waited a couple minutes and reconnected it.
Now usb is working again. Oh, and I didn’t lose any of my presets.
