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In our blog, we used to use the normal WordPress editor to publish any new post to our blog, but now we aim to use a unified skeleton for each post where each post is divided into 4 or 5 different sections.
We used wpbakery to implement the general post-template since our main theme pages were build using it.
The main difference from HTML point of view between the new post page and the old post page is that in the WordPress normal editor (old page) we have a series of P tags with some H2,3 tags and image tags, all of these are encapsulated inside one content div.
While in the new implementation each section title is encapsulated in two divs and section body in two divs. (see the sample page attached below to get a better view of what I mean)

I tried to use different article extraction tools and they all were able to extract the page content without any problem.

The main question now is: does implementing these changes to the post structure using wpbakery affect the SEO rank in any bad way

old post sample : https://bit.ly/3dBVyBb

new post sample : https://bit.ly/37YsfaW

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Google has often said that proper HTML formatting and semantic tagging is important in how they understand content on a page. They often use this in order to extract and understand the important parts of a page. headings tags like H1s and H2s are still important. Google goes to great length to identify which parts of the page are "primary" content and which parts are "secondary" and they use many heuristics to do so, including semantic HTML. But from what you describe above, the only difference being "each section title is encapsulated in two divs and section body in two divs" it doesn't sound like this would cause issues with how Google understands or parses your content.

Here is a resource you may want to review: https://developers.google.com/style/semantic-tagging

In addition you can use a tool like this in order to see how your page renders: https://codebeautify.org/htmlviewer/

I would also highly recommend testing the new template before launching it site-wide. What I would do is launch the template across a handful of pages, maybe 1k depending on the size of your site, and come up with a control group of similar pages but keep them on the old template. After launching the new template you'd want to track and monitor your rankings, clicks, impressions, etc. to see if there is any difference. Good luck!

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