In order to Delete Parameters or delete anything you need to highlight the item in the tree control. then press the X delete icon.
You will get a message box to make you really want to delete this item. If this is a job then you may need to extract that job again. If you delete a project then all jobs in the repository are deleted which were extracted from this project.
Only deleting a parameter under a job name under Jobs will delete the parameter in the job on the DataStage server. This is the only delete which updates the DataStage repository.
Next you will get a message box telling you DataStage was updated.
If you try to delete a main subject area then you will get this message.