My site is getting deindexed. Please help

Do some internal linking, and push them via speed-index or other indexation tool, probably will get half of them back.

This and you need to start building some backlinks to the top-level pages, as well as some of the inner pages. The site is only 7 months old, so you need to increase the authority with backlinks and internal linking.
 
I think google has been having problems for a long time, the same thing is happening to me :(
 
How do you know there was no negative SEO with surety? There may be some bad links that you are not able to find.
 
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