The latter type case is what the article is talking about though. At the same time, as the article also discusses, it's unlikely to have actually been caused by malware vs something like a poorly packaged update.

Backup tools should deal with file changes lacking corresponding metadata changes despite it being more convenient to say the system should just always work ideally. At the end of the day the goal of a backup tool is to backup the data, not to skip some of the data because it's faster.