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What steps should I proceed to tell Google about my migration from HTTP to HTTPS (there is 301 valid redirect is set), nothing I can see in Google webmaster (they have migration, but it is saying they do not support such migrations). Eventually I just setup ssl cert and set nginx accordingly and after two weeks I see nothing indexed and nothing in search. Is this expected?

Also, how bad for SEO subdomain.domain.com? Domain goes to subdomain.domain.com with 301 redirect..

Much appreciated!

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Yes! It is expected, but not so obvious why...

You should add a new property in GWT, i.e. https://www.example.com

Note the s in https.

Google treats them as different sites. Keep your 301s from the http site.

The Search Analytics numbers for the http propery in GWT should decline while the https property Search Analytics numbers should rise.

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