Major canonical issue on e-commerce site

Hi! I have a client with an e-commerce site, when I crawled it using Screaming Frog I found 38000 pages which 31000 are canonicalised and non-indexable. Looking at the page it seems like the CMS must be creating a duplicate of a product page and marking it as non-indexable and canonicalised, the pages has a different bread crumb structure so I'm guessing that might be the issue.

My question is, how do I go about solving it? Since the pages are marked no-index they don't really hurt but given the massive amount of canonicalised pages it would be nice to get rid of them. Do I 301 redirect the canonical page to the "real" page? Or should I remove them altogether? But I want to make sure not to loose any traffic/links to the site.

Happy for any advise on how to clean the site up! Thanks so much!