I am having a similar issue as user agathamalina, my products do not show on the product category page. Upon reading her thread I realized that I too had updated files that were showing as outdated. I had someone look at this before I saw this thread and he said it was a theme issue and I have to agree as he changed the theme and one of the products showed up. We deactivated plugins and saw that did not fix the issue, then he changed the theme that is where we saw some change. I have attached screen shots you can see your theme and another theme and it working on another theme.
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