We are running on Magento CE-2.3.5 open source and keep experiencing products disappearing from the website.
When we make product changes/updates and we run indexer:reindex; all products are in their correct category assignments but eventually we notice the products begin to appear under different categories that they are not assigned to.
For an example: A Category has 11 products assigned (6 enabled / 5 disabled) and we see the 6 display on the website as we expect. Then we experience the issue with products being removed/disappearing from the website and then this category becomes 11 products assigned (6 enabled / 5 disabled) but 7 products display on the front end. This extra configurable product does not have this category assigned to it and neither do the simple's underneath it. In order for us to correct this issue we must run the indexer:reindex.
As far as individual product display is concerned: product is enabled, assigned to websites, assigned product to categories, product stock status is in stock, and verified product visibility.