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Everything works fine with the xroot protocol :

$ xrdcp --cksum adler32:print root://xrootd-ccaffy-dev01.cern.ch//tmp/non-empty-dir/does_not_exist.txt -
[0B/0B][100%][==================================================][0B/s]  
Run: [ERROR] Server responded with an error: [3011] Unable to open /tmp/non-empty-dir/does_not_exist.txt; no such file or directory (source)

I'll investigate but I'm sure I will find who the culprit is ;)

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