Hello,
We apologize for the issue you are facing with your subdirectory setup and how it is being indexed by Google. It seems that Google is treating the posts from your subdirectory as part of the main site, which can happen due to how the URLs are structured and indexed.
Here are a few steps you can take to help resolve this issue:
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Interlinking: Ensure that you are interlinking between your main site and the subdirectory appropriately. This can help Google understand the relationship between the two.
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Sitemap Submission: Make sure that you have submitted separate sitemaps for both your main site and the subdirectory to Google Search Console. This will help Google crawl and index them correctly. Rank Math automatically creates a Sitemap Index for your website, which you can find at https://yourdomainname/sitemap_index.xml
.
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Canonical Tags: Use canonical tags to indicate the preferred version of your content. This can help prevent duplicate content issues. You can easily change the canonical URL using Rank Math’s meta box.

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Check Google Search Console: Look for any manual actions or indexing issues in your Google Search Console account that might be affecting how your subdirectory is indexed.

If these steps do not resolve the issue, we recommend replying to your ticket, and a human agent from the Rank Math Support team will assist you further.
Thank you for raising this concern!
Sources:
Why Did My Website Disappear From Google Search? » Rank Math
Why Did My Website Disappear From Google Search? » Rank Math
Hello,
I have updated the sensitive data as requested. Can you please check further?
Thank you.
Hello,
Thank you for your query and we are so sorry about the trouble this must have caused.
Checking your subdirectory website, there aren’t many posts shown there. Can you please share the affected post URL here so we can check further from our end? You may also share a screenshot of the SERP so we can understand the situation further.
Looking forward to helping you.
Hello,
Since we did not hear back from you for 15 days, we are assuming that you found the solution. We are closing this support ticket.
If you still need assistance or any other help, please feel free to open a new support ticket, and we will be more than happy to assist.
Thank you.