Hello,
If we understand you well on this page, you expect to see relative brand products (and by the past that's use to work)
From your elements several possibilities and points (not all link directly) to check :
1. Maybe your update have partly messed up the difference between categories and subcategories
=> Try the "Rebuild" button (in Products => Categories)
2. Check that you product is
still affiliated with their relative products category (or categories).
3. Process a test with a default template (like ProtoStar) to see if that solve your issue.
Awaiting your returns to progress on your subject.
Regards