Google "usb recovery software" to find a way to get a copy of the file (hopefully intact) off the flash drive onto a reliable drive. It might be a quick and simple repair to the file system, it might be a patchy mess of disconnected and missing bad blocks. If the file was saved or moved more than once on the drive then it might be possible to restore one of the earlier autosaved/cached versions instead.

Google "pdf document repair|recovery software" to find something which can reconstruct damaged/corrupted pdf files. Better to work off a copy of the file instead of writing changes to the original, just in case multiple attempts with different softwares are needed. Also much faster.

If it's too much hassle then you might find it faster to just scan the document again. If the USB stick is too messed up and unreliable then you might be able to recover the scanned file from the Recycle Bin (or by running disk/file recovery software) on the computer attached to the scanner.