The best utililty for this is Robocopy (Rboust File Copy). It's a free MS utility that offers many options for copying files & folders. There are switches which allow you skip open files, you can also retry the file 'x' times before skipping.
I use it all the time when I'm doing server migrations. There is a GUI version available, but I prefer to use it from the cmd line as it's easier to see what's going on. If you download the GUI version, just open a cmd prompt and type robocopy for the DOS version.
A word of caution, the /MIR switch allows you to make an exact duplicate of the source path in the destination. If the destination directory isn't empty when the copy starts, the existing files will be deleted.
