Steam Hacks
Steam Cloud
Removing elements from steam cloud
Synced files can't be deleted easily (they'll be redownloaded).
Quick summary:
Overwrite the files while cloud is disabled to trigger the sync conflict dialog
The dialog allows overwriting cloud files from local files. Before choosing an option, deleting the local files and uploading them to cloud allows deleting them from the cloud
Source: Finally! A method to DELETE files stored in Steam Cloud servers! - Steam Users' Forum
