hey @markus007 @slide cross-posting my answer from GitHub · Where software is built
It was opened some days ago in Creation of subfolders using desktop client after a move across shares can lead to duplicated folders. · Issue #28018 · owncloud/core · GitHub and a fix is already in the making (Fix cross-storage move info when moving between two received shares by PVince81 · Pull Request #28022 · owncloud/core · GitHub), keep an eye in the core issue for updates.
Thanks for reporting! 