Move all the files you don't want (likely all the files in the data Folder) to another Folder before copying the backup files into place. After the copy, run Data Integrity Checks in all the modules, and print the major reports to confirm the numbers are what you expect.
It's usually well worthwhile checking with your Adagio consultant when you find yourself in this position, since a mistake in the process can generate days and days of work.
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Andrew Bates