We have 1 out of stock product and 78 in stock products. But in layered navigation I am getting In stock(79) which is wrong.
I have set "Display out of stock product to YES" in admin configuration.
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It seems like you use Product Stock Indexer. Try to do these steps:
bin/magento indexer:reindex cataloginventory_stock in console
bin/magento cache:flush in console
flush varnish cache (additional, if you use one)
sudo service varnish restart in console