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First time I have heard of Windows Explorer failing to copy files without at least giving an error message!
Did you copy/paste the Calibre Library folder or just folders from within it? I would normally just do a copy paste of the whole library folder. If it is a path length problem then as long as you make sure that the path length is no longer on the target system I would have though that you would be OK.
As to Save to Disk not saving large files I do not think this is a known problem. If you get an error message its contents might be relevant. Also if they are PDF files you might want to consider disabling the PDF Writer plugin as that has been known to cause problems.
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