Not really a huge mystery. Now that we know you are using WooCommerce 4.2.2 then we know you aren’t working with a version of WooCommerce that isn’t 100% compatible with the PPOM plugin. Currently, the PPOM plugin (free version) is compatible up to 4.1.x. PPOM Pro is currently set to work with 4.0.1.
Best practice for updating plugins is to ensure that the plugins you have installed, especially plugins that have a dependency on other plugins, are only updated to the version that your other plugins are reported to be compatible with. In this case, you should be running WooCommerce 4.1.1. If you have PPOM Pro installed then you should be running WooCommerce 4.0.1.
There might be a change in WooCommerce 4.2.x that has affected how variations are attached to products. Although I don’t think Automattic would make a drastic change to core hooks like that without a major reason (e.g. security fix).
There may also be a problem with your WordPress / WooCommerce installation. You may have some malware, have been hacked or you may have a corrupt database.
You may have a PHP configuration issue. Maybe your max_input_vars is too low.
You might be using invalid characters in your PPOM meta group, or the values that are entered for the product, that are being stripped out when emails are generated and sent.
There are many reasons why there could be an issue with your website.
You should enable debug
mode for WordPress / WooCommerce, run some tests and see if there is an underlying issue.
https://docs.woocommerce.com/document/woocommerce-product-search/api/debugging/