There should be a filesystem check program to clean your dirty drive. fsck in linux. chkdisk.exe? in windows (older versions anyway). Probably some .exe in C:\windows\system\ (or system32 or whatever the latest moved things to)
Alternatively right mouse click on the drive/partition in windows explorer. And it should offer some properties / tools there abouts. Linux has been my primary since 2002, so a little rusty. The issue will likely repeat for you, so you might as well acquaint yourself with recovery methods. Tis the nature of external drives. Although reformats are a quick way to optimize / defrag a filesystem if you've got the room to shuffle the data.