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Hi there I would run through this migration guide to make sure that you took every step in moving the old site. It sounds like you did this in a messy way and I'm not entirely sure what you did. If you are moving content, 301 redirects need to be in place immediately. I would also read into Google's resources on URL changes. This is all kind of cloudy, so make sure you run through the resource above and that should help you. Let me know! Good luck!