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Thanks everyone for the confirmation!

Thanks for the Respond,

The Root Domain/ Homepage was ranking for the the main search term until Feb 9th, then after that the Sub Page was only ranking for the same search term.

1. There is no duplicate titles or pages. 
2. The Homepage is indexed, as it still ranking for other search terms, and I also search in google site:www.mysite.com
and still there. 
3. There are no canonical issues. everything is Redirect to the Https, and the Https was ranking as for couple months until Feb 9, 
4. No duplicated through index.html, default.html 
5. 70% of the links are point to the Homepage.
6. Our Anchor Text distribution has only branded keywords, city name and the website, there is no commercial keywords.

Thanks

I am just wondering if you disavow a link from google webmaster to a certain website. Does that hurt the other websites ranking at all?

Thanks

What do you think can be causing issues that my main homepage is not showing on search results for the main search terms, only my sub-pages are showing up like the reservations page.

ps. I did not get a manual penalty action email.

Thanks,