i had a variation on this theme. it went something like this.
external usb formatted ntfs by a win7 machine
attached it to a qnap, pretty recent firmware (3.5.1 or 3.5.2)
copied 1.5tb files from a raid volume to the usb drive via the shell, all to one folder off the root. .
copied more files.
detached it properly
attached it to another qnap.
could not copy files from it using the shell or the smb share. folder not accessible (similar to symptoms seen on this thread), no files visible in folder.
updated to latest firmware (3.5.2)
no change.
detached the disk and hooked it up to a windows machine.
ran chkdsk/f on it. it found errors (perhaps corruption, i don't recall) in the security descriptors and corrected them.
connected it to the qnap again and i was able to copy the files.
hope this helps someone until qunap fixes it.

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