_variation_id set to 0

We’re having an issue after a server, core and plugin update where some orders or coming through without the variation data and the customer is being charged the system default price. We suspect front-end caching (we were using a caching service), but this is weeks later and it’s still impacting 1-2% of orders.

-On wp_posts and wp_postmeta tables everything looks good for both cases. (On this table usually is general info about the order: payment_info,address,name etc)
-On wp_woocommerce_order_items also everything looks good. (On this table there is a reference of order_id. Also this table contains all the names of products on the order)
Example : 724573 NAME Purple Nitrile Exam Gloves – Medium, Box of 100 line_item 9296466

– On table wp_woocommerce_order_itemmeta I do see the problem. In the broken order some of the fields of this table are not set. In this example I do see _variation_id set to 0 also _wc_cog_item_cost is set to 0.
– In all the cases that the order is broken the _variation_id is set to 0.

So we do prove it on the db level. I am still working on trying to find out why sometimes this values are not set, but the other values on that specific meta are, for example pa_amount, size-color etc.

This started after we did the following upgrades :
The web server we are using is nginx
Ubuntu 16.04.4 LTS

This started after :
Server patching Ubuntu 16.04.4 LTS
Upgrading from php7.1-fpm to php7.4-fpm
Full wp and woocommerce (versions) and plugins upgrade.

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