Removing any object from a Procedure timeline through the workspace or Structure view and then immediately closing E-Studio does not prompt to save changes. Upon opening the .es file, the item remove remains on the Procedure timeline.
Internal Design Flaw.
Manually save your experiment prior to removing items from a Procedure.
Update your system to E-Prime 1.1 Service Pack 2
This article applies to:
E-Prime 1.1 Service Pack 1
E-Prime 1.1 Service Pack 2