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Lot of sync errors are due to path. TrSync algorithm use something content_id & revision_id to identify changes. But in move situations, TrSync can miss it because content_id and revision_id rely on files whereas they have moved. See this fix : 859d23c
A better approach could be consider first files by their path. And use content_id/revision in second time.
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enhancementNew feature or requestNew feature or request