There is a situation where WordPress tells you that it has updated the permalink structure but doesn’t .. similarly, there is a situation where it tells you to copy code into your htaccess file but never actually displays the code
It turns out that these things happen because of incorrect error handling by WordPress. That is, the permalinks aren’t updated because of something wrong with the server, but the message saying that the permalinks have been updated when they haven’t is an incorrect thing on WordPress’ part.
Please see more info here:
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