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My client's CMS uses an internal linking structure that includes index.php at the end of the URLs. The site also works using SEO-friendly URLs without index.php, so the SEO tool identified a duplicate content issue. Their marketing team thought the pages with index.php would have better link equity and rank higher, so they added a canonical ref tag, making the index.php version of the pages the canonical page. As a result, the site dropped in the rankings by a LOT and has not recovered in the last 3-months. It appears that Google had automatically selected the SEO-friendly URLs as the canonical page, and by switching, it re-indexed the entire site. The question we have is, should they change it back? Or will this cause the site to be reindexed again, resulting in an even lower ranking?