The company has been unable to reproduce the problem but here is the statement they provided to iMore on the issue.
In an extremely small number of cases users have reported that music files saved on their computer were removed without their permission. We’re taking these reports seriously as we know how important music is to our customers and our teams are focused on identifying the cause. We have not been able to reproduce this issue, however, we’re releasing an update to iTunes early next week which includes additional safeguards. If a user experiences this issue they should contact AppleCare.
It’s unclear if the problem, which seems to affect a very small number of people, stems from Apple’s FairPlay digital-rights management and the iTunes prompt confusing users to inadvertently delete their previously matched songs.