After removing the issues and clearning the website, you need to use fetch as a google bot option in your search console. Approx 90 days are taken to get the some of lost ranking.
Website is usually penalized by either unethical SEO practice or mistakenly inserted hidden/semi hidden text. Sneaky Javascript redirection may be the cause of deindex of your website. While implementing SEO on website, you should be very careful about the background and font colour.
I worked on website of online book store. It had been de-indexed in Google because my developer tried to change URL structure. He made updates in .HtAccess file. Instead of using 301 redirection script he used simple javascript redirection which make all pages “Doorway page”. Now this website (Approx 3,00,000 pages) has been spamed and de-indexed completely and traffic has gone down to Zero.
After rectification of all errors, google starts re-indexing your website with in 90 days.
Keep in mind
Do not do offpage optimization while re-indexing of your website. Try to create more appropriate internal links. In the period of re-indexing, you should add more and more fresh and genuine content with contextual internal linking. Offpage optimization should be started after 6 month of re-indexing of your website.
I hope you have gotten what you were looking for.
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