If File Synchronization crashes, then give it more memory. This increases the heap.
If it's a PPC program, then you can also increase the stack. Open 'cfrg' resource 0 and change App Stack to a larger value.
I synchronized a directory with 20 levels deep without problem.
Before you synchronize, you should look for potential problems, like locked icon files and locked invisible files, which make some programs crash.
Some file copy problems are caused by invisible files and folders, for example made by file sharing, OSX or Windows.
Icon files can cause trouble because they may not be added to the total file size and then it's miscalculated and may cause overflow in the progress.