Are you open to using PowerShell? This could be done in a single line.
Run this at a PowerShell prompt and you'll see how simple it is to identify which files you'll be to overwriting:
Get-ChildItem -Path "\\servername\sharename\target" -Recurse -Filter "target.file" | Select-Object FullName
From there, it's just one more command in the pipeline to copy your local target.file to overwrite the existing ones.
If target.file might exist in directories not named backup and you want to leave those alone you may need one additional command in the pipeline to filter those out.
edit: fixing quoted text, forum ate a backslash n.
There are no special teachers of virtue, because virtue is taught by the whole community.
--Plato