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.
While initially Apple Music was blamed for the problem, it appears the issue may lie with iTunes. We'll let you know if Apple makes any headway in determining the cause.
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