Our CMS uses an internal linking structure that includes index.php at the end of the URLs. Some pages of the site are also accessible using SEO-friendly URLs without index.php, so our SEO tool identified a duplicate content issue. Our 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? The marketing team only made the change for one section of the site leaving another section with the truncated URLs as canonical. Should we continue to leave those alone? Is there any downside to having part of the site listings using SEO friendly URLs and the other part using index.php?