I tried everything I could think of and then had a 45min chat session with QNAP tech support. 1000 points to QNAP they solved the problem. Apparently a particular update along the way changed an important Samba setting. The fix was to SSH into the NAS device and the run the following two commands:
/sbin/setcfg Samba ADS NO
/etc/init.d/smb.sh restart
(the tech used PuTTY to SSH in)
Basically this allowed the transfer of a file without properties. I'm guessing the files that weren't copying (only some of them) had extra sidecar information that was causing Samba to reject the file (old XMP files or Mac files?).
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