I just added a new category to my store, It then said running cron index and to flush the cache. As I did this. All products disappeared from the store.
I have ran the commands php bin/magento indexer:reset and php bin/magento indexer:reindex but the products are not returning. The run time of the indexer is 00:00:00 on all jobs, so something is not right.
Before creating the new category, we also setup a new Inventory Source and Stock. When doing so, the new stock had website * Main Website (base) selected, which moved it from the “Default” stock.
Deleting the new stock, which means removing the “Default store” from the stock, followed by a reindex returned all products to the website.
What I find interesting is, that none of these products belong to the default stock. So you need to leave that alone.