Other Configuration Manager-related features and issues
Sure, it works to copy the files from cd.latest folder.
For the problem we're facing, the files may were deleted accidentally. To know who and when the files are deleted in future, we may enable file auditing.
For more details of enabling auditing, please refer this article:
https://www.manageengine.com/products/active-directory-audit/kb/how-to/how-to-enable-file-and-folder-access-auditing-in-windows-server.html
Note: This is not from MS, just for your reference.
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