Permalink problem with subdirectories

  • I have read several past posts here. I am using a shared hosting acct. When I change my permalink structure on my main domain, I lose my other websites that are sub directories. I see some answers in past posts but they are not working for me.
    Also, since the subdirectories are not really related to the main domain, am I making a mistake for SEO purposes? Should I just shell out the extra hosting money?
    I am using single WP for each site. Is this the problem maybe?

    Thank you in advance. I am newb to WP.

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