Could you clarify how you're copying files? You mention Retrospect, which I know is automated backup software, but said that it's "extra". The description of deleting a folder then recopying it suggests you're doing something simple like drag-n-drop in Windows Explorer.

If you're doing a simple copy, the DOS 'xcopy' command might be useful. I use it to make mirrored backups on the server and at home. It has a /C option that tells it to continue copying even if there's an error, which would get you past the problem of locked files. You can get info on all the options by typing 'help xcopy' into a cmd window; a typical line from a batch file would look like this:

xcopy c:\clients\*.* \\VAULT\Robert\Mirror\C\clients\ /s /c /Y /D /Q

\\vault is one of those standalone networked hard drive boxes.

Xcopy has a tendency to produce ever-growing backups, because it doesn't purge files you've deleted at the source. Every once and while you'll need to do that thing with deleting target folders to force xcopy to start over with a clean backup.