how to refresh wordpress permalink settings? (without admin panel)

Add flush_rewrite_rules(); to your theme’s functions.php, load the page, and them remove it. It is very inefficient to have that run on every page load.

Hopefully your edits to the options table are sane. If not, that will not work.

Caveat: I think that functions.php is adequate. You may need to add it to a plugin or a mu-plugin file if that does not work correctly.

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