When an element under version control is deleted, it is still shown in the elements tree, marked with a gray icon (see section Integration with the Elements Tree), although it does not exist anymore in the server, so its details cannot be accessed from the Administration Tool. When deleting an element, it is possible that other elements are also deleted (because they depended on the element). If those elements are under version control, they will also be shown in the elements tree, marked with a gray icon.
Checking in a deleted item will delete it from the version control server. Checking in a folder or a whole database will remove all the deleted elements that it may contain.