FYI, this error still occurs for me in 4.1 SP6. The workaround I found for it was to delete the folder or item within the file system as outlined above (note that I am not using the default file location, but this works when deleting from the file location I am using). I was then able to delete the item from within IDT. A reload of IDT did not automatically remove the item, but a delete would then work.
Hope this helps someone else with similar issues,
Tom