Refreshing permalinks via Settings or via WP CLI – difference + what happens really?

When I run wp rewrite flush on my server (after deploy where .htaccess is copied over) my translated category pages throw 404.
When visiting Settings -> Permalinks everything is fine again.

I’m using Bedrock

So it seems I do not really understand what happens when you visit Settings -> Permalinks and what happens when you run wp rewrite flush.

Can someone help with explanation/links?

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