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Once more I answer my own question. I'll try not to do so anymore in the future.

The problem has nothing whatsoever to do with SAGE itself. It's caused by a sloppy configuration file used for rsync. As a result there is a confusion between the root folder /media/ and a subfolder media/ deep within SAGE. It took some time for me to locate the folder .../media/... within SAGE, but then I saw that this folder was indeed copied, but left empty by rsync. From there on I quickly found the reason why.

I'm sure there's a simple command that could have told me where to find media/ in a second, but I'm far from a linux wizzard, and the SAGE folder has a quite overwhelming tree structure.