seo – Google has deindexed portions of our page after copying the content

This year, our website has featured in a number of leading design articles and has subsequently been copied in-depth. Now, Google seems to have deindexed parts of our homepage (and perhaps other content), which worries our SEO and CTR rankings.

Moreover, it no longer reads the key parts of the page to present in SERP, rather converting our navigation into text. The results, as you can imagine, are very poor (see image).

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We are a Christian organization and we do not wish to pursue copyright infringement.

What can be done about this?