Avast is detecting the malware, and its suggesting to move it to chest (quarantine), so why not do it? Or, just delete that file. Clearly, it’s a malware file, and therefore, deleting it won’t have any effect on the rest of the files in the pen drive. Just delete the detected malware file. Why are you trying to repair it? It’s not an important file, it’s just a malware file.
If you suspect that the drive might still be infected, scan it with Avast again.
To make sure that there are no more malware inside, you can scan with other security software, like MalwareBytes Antimalware free version, or, as suggested, you can also download an antivirus rescue disc, and scan with it. Kaspersky Rescue Disc is an excellent rescue disc. You can also use BitDefender Rescue Disc too.
You can also scan your whole computer with this disc to make sure that the malware has not infected your computer.
For protection from malware from pen drives, I will also suggest a free software, an anti-malware specially for pen drives. It will function very well along with your resident antivirus. The software is
MCShield: http://www.mcshield.net/
Its detection capabilities sound great, and the product itself looks good. Although, there are no independent tests as to how good it is. But, it definitely looks good. You can install this too, and scan the pen drive with it.
Also, another tip. To prevent malware from pen drives infecting your computer, I would suggest the use of Toolwiz TimeFreeze, a virtualization software, which is excellent.
When you start Toolwiz TimeFreeze, any changes you make to the computer won’t affect the computer in real. So, just put your pen drive then, and scan it with an antivirus. If malware is found, remove it. And then take pen drive out, and then reboot the computer. No change will be made to the computer at all.
Suggesting this, because sometimes, even with autoplay option turned off, the malware inside pen drive can cause it to open automatically. Once the pen drive opens, the malware can infect the system, and some of these malware can be really nasty and hard to remove. Therefore, this method offers good protection.
Good luck.