“Hide out of stock items from the catalog” hides In Stock products

Howdy!

There is an issue with “Hide out of stock items from the catalog” setting. When it’s active some in stock products not visible (not showing) in shop, in product category/subcategory and search.

I tried to deactivate all plugins and use Storefront theme but nothing.
Also Clear transients, Clear template cache, Regenerate product lookup tables, Update database doesn’t help.

In order to overcome the problem the problematic product should be made featured and back. That’s the only way I found to get the product visible.
However since the shop has 10k products this is not solution so any help appreciated.

Any ideas what can be wrong, what else could I try to get all In Stock products to be visible in shop?

Thank you

P.S. WordPress 6.0 / WooCommerce 6.5.1