Without more information, it's hard to craft an exact solution. But you can use C# (or any of the .NET languages) to peek into a workbook and get a list of sheets in that book. You could write an entire console app that performs this for you. Alternatively, you could use SSIS and build a package that uses a series of scripts, workflows, and file tasks to move the workbooks around. There are a few different ways to do this, but if it were me, I'd start by searching the web for those types of topics and see where that gets you.
-G