I have EE configured to save my templates as files.
I had several different template groups that I deleted via FTP. I clicked on "Synchronize Templates" and ticked all the boxes, and hit submit. I no longer see those templates listed under the Synchronize Templates page.
However... The template groups are still listed under the Design --> Templates --> Edit dropdown menu. There doesn't seem to be any way to get rid of them.
I have a feeling it's because I have Save Revisions turned on. I can see old templates that have clearly been deleted, so opening them up in the EE editor will show an empty file - but with several revisions available to restore.
Is this an ExpressionEngine bug, or is there any way around this?