Well, antivirus *does* delete a few virus files, but your files and folders. It so happens that your original folders on the pendrive gain OS privileges, when the virus is being healed/quarantined by the antivirus. And so, these folders go hidden(and not deleted!!!). You can very well see these hidden/missing folders, with an acquired lock on Ubuntu. But then on Windows, you can’t see these folders even if you check “Show hidden files and folders” in the “View” tab of “Folder Options” on the toolbar. So, to gain an access to such folders, you can try one of these 2 options:
1. If you’re lucky enough and remember some or all of you folder names, you can type the path for the same in address bar of Windows. For ex: K:/New Folder, if the “New Folder” is the folder which has gone missing. It works for Nested hidden folders too viz. K:/New Folder/Songs and Bingo! You’re inside the “Songs” folder. Well, these folder names need to be exact and Case-sensitive though. You can’t get an access to “Songs” folder if you type in “songs”
2. You might not always be lucky enough with your folder names, as in step one. Well, step one won’t be required, with this particular step. You simply go to “Folder Options”, go to “View” tab and uncheck the option “Hide protected operating system files” and click on “Yes” in the dialog-box that appears. And Magic…!!! You see all your missing folders, back again :). To avoid doing this step again n again everytime you insert the pendrive, simply cut-paste the contents from the hidden folder(once you get an access to it) to a new folder.
PPS: I could have posted some screenshots. But I’m posting from Ubuntu and am very lazy to “Google” the screenshots n upload here. Good Luck.