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I may be misunderstanding your question, but from the screenshot it looks like the folders are expanded and marked as different even though no items are shown inside them.

In that case, the folders are likely marked as different not because of their timestamps, but because they contain items that exist only on the left or only on the right. Those items may be hidden if you have enabled options in the View menu to hide identical items or left-only / right-only items.

If you want to ignore left-only or right-only items, you can use a folder filter in the Select Files or Folders dialog.
For example, set Folder → Filter to:

fe:LeftExists and RightExists

This limits the comparison to files tha…

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