Thanks @ogoffart for the hint!
I checked my synced folders and moved the database files while I noticed that my file system somehow was broken. There where two files ( “.csync_journal.db-shm”, “.csync_journal.db-wal” ) that seemed to be broken (Ubuntu gave me an Input/Output-Error on these).
After executing chkdsk on windows (it was a ntfs partition) everything is fine now.
So I guess this wasn’t directly related to/the fault of owncloud, was it?