Replace zero size files?

I have a bunch of files in a hard drive, some of which, for some reason, show a zero file size. I have another hard drive where these files are stored, but they are not in the same folders, and are somewhat unorganized, but have the correct file sizes, and can be opened.
I need to overwrite the zero size files with the good files, but I can't just copy folders. Instead I need to basically look at each file individually, and copy the good one over the bad one.
Is there a way to automate this? We are talking about 20,000 files or so, which otherwise will be my full-time occupation until I keel over at my desk and pass on to the next life...

I don't think there's a good way to do this without a custom script, especially if the files are on a separate drive and have a totally different folder structure.

A custom script... well, I would be happy to pay for one to be written, let me know if you or any of you want to take this on :idea: