The boards or assets in a workspace are also moved, renamed, or deleted if the corresponding folders or files are moved, renamed, or deleted in your file manager (Finder on macOS or the Air Flow file browser on Windows (beta)).
If any user with the Air Flow app takes these steps, the changes will reflect for every workspace user + visitor. To prevent changes in your local environment from syncing, use the Selective Sync feature to exclude a set of boards and/or libraries from sync altogether.