Yes, I notice almost all antiviruses, antispyware, and antimalware scanner programs I have tried like AVG, Avast, Immunet etc sometimes delete files which are known to be virus free like Winamp media player because it thinks it is a virus.
Yes, once Norton deleted my firewall, and I ended up with a nasty virus infection that, Norton could not detect or remove even with updated definitions..
This is why it is a good idea to keep back ups of your files since Anti-Virus can think your homework, and other files contain viruses.
But, I set my antivirus to notify me before I quarantine files instead of delete, so it is easier to restore them if my Antivirus deleted files which are clean.