When you upload the files, overwrite all files always. Don’t ever skip any file.This will avoid breaking your own website.
You should have backup the whole of your drive to a Pen Drive or something similar before you do anything.
Nowadays, you can even backup to Github , Bitbucket or any online SVN code repository service if the files are non sensitive. It will be there perpetually and you can share your codes for even faster troubleshooting. For files that you do not want to share, you can put it in .gitignore file. It will take some effort to set it up but once you do, you will never regret it.
This is just a friendly advice to prevent similar situation happening to anybody else.
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