DirReplacer is a small file management tool that allows you to replace, copy, integrate, backup and remove directory file contents with the contents of another. Project has been abandoned.
This is a straightforward non-batch processing enabled tool so you are limited to performing file actions one by one but does allow the addition of multiple directory replacement paths as well as the section of a specific directory to replace.
That said, DirReplacer will allow you to update several backup folders within a single operation. Additionally, while replacing the main folder files, it will also be able to replace all the sub-folders as well.