Site structure question

I would be thankful to hear your opinions about next situation.

The current website is made in custom CMS that was never planned to be SEOed.
But changing complete website with integrated payment module and the established system seems like too much work.
I am aware that it would be the best option.

So the alternative is to leave the site as it is and create a new section that will target related keyword. Based on WordPress, for example.
Question is: will and how the "old" part of the site affect SEO performance of optimized pages in the new section?


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