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Hi Phil,
Since you mentioned that the time when the user log on to Windows equates to when the documents are deleted and the issue happens to the specific user account regardless of the computer, I was guessing that some user specific settings(GPO, task schedule, etc...) delete the file from local computer which results in files being deleted online as well.
However, I also noticed that this issue only happened several times in 12 months instead of reproducible every time user log onto Windows, so the setting may be not related.
Given the situation, I would suggest disable syncing library for this user and monitor to see if this issue can be reproduced. If not, we can confirm that this issue is related to local environment.
Best Regards,
Vincent