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After a couple of months of not updating, I updated my local copy of WOU to 9.3.1 from 9.2.1.

Then, after successfully running the update-download, the folder "wxp" was still located under "client", although I have "Clean up download directories" checked.

Is this by design, a bug or a side-effect of the "superseeded"-changes?

Checked software-versions are Vista x86, Windows 7 x86+x64, Office 2010 eng+ger.

It is not caused by the problem with the superdseded updates. The cleanup optiom will just clean up the repositoty for a specific OS (e.g. KB2982791 was deleted by this function). It won't delete a complete repository. After the remival of support for a specific product, you will have to delete that folde ("wxp" in this case) manually.

It can not delete wxp because the code has been removed. wxp does no more exist as an option in WSUSOU. Delete it, it will never come back.

I assumed WOU would remove these files automatically in 9.3+. Guess not.

Are there XP-only files in the other folders too, or are they just in the wxp-folder?

IIRC XP 32bit only used win and wxp. Since win is still in use deleting wxp is sufficient. Other things are either shared (.NET stuff) or already removed (Defender).