We are taking your USB drive, yes? Well if it's a flash memory drive always right click on the drive in Windows Explorer and left click "eject" before removing your drive. What you explained never happened to me but happened to my late friend Walter (RIP) who insisted it never happened to him after he followed these instructions.
You can try using one of the flash drive recovery programs to repair a corrupt drive. I have used these in the past with excellent results for friends. I forget the name of the program, sorry but I think many brands work very well.
Hope that helps.
-Dog