I added other files locally and after rerun the update and the error disappeared and everything ended without any error or warning.
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Should I be worried?
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Maybe there is any additional tests or repair that are triggered on local change of data but not triggered if local data equals to remote data? Also here: Warnings like: "Duplicate path detected" the issue was fixed either after I added data to local data OR folder contained space character on the end and removing it fixed the issue. Maybe @kenkendk can answer this?