After some further crashing and restoring via USB, I gave up and left the sync problem (I didn't have any files left to sync, LOL :-)
Interestingly enough, a few weeks later, I tried to sync again with ethernet and it worked fine. So either it depended on the state of the player, or there were general network problems in the university network at that time, which only manifested themselves in the described way.
Either way, the problem is gone without any changes on my part whatsoever.