I copied all of them at once but I used a program called Teracopy and I didn't have any issues. That is another thing people could try.
Doesnt everyone use Teracopy or similar these days, have for years, of course fragmentation will occur copying multiple files at once..
its a precaution, just let someone who knows better answer it.
He does know, and off course saves work, all they did was add eshop compatibility like kyorge123 said