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Was the card inserted into the computer's SD reader, or was it in the phone and you were connected via USB? Massive data transfers might cause more risk of data errors or loss--I usually prefer to copy large groups of files in smaller batches, rather than en masse.
Did you use the "Move" function or the "Copy" function? In this kind of situation, Copy is preferred, because it leaves the original files alone, while Move will delete the originals once it thinks the transfer is complete. This can obviously be a problem if the files weren't moved properly.