The partition delete command appears to work properly on an EDIF-based design (search * -type partition indicates the partition has been removed). However, after the project is closed and reopened, the partitions are still there.
Solution
The "partition delete" command should not be allowed on partitions that are on EDIF design units, as these partitions should only be created and deleted in the third-party synthesis tool.
The "partition delete" Tcl command has been fixed to correctly reflect this limitation in the message returned in this situation.