There are two ways in which you can perform an apply to commit a rule deletion in SMARTView.
1. Through the SMARTView GUI
An apply can be performed by opening an existing rule under the Group in which you deleted your rule (right click on the rule name > Properties > Work with this rule), then clicking on Test/Apply. This will open a new window in which you can perform an apply, pushing any changes (your deleted rule) to the BES server.
2. Command Line
From an SSH session to the BES server as ppadmin, run the following command to run a rule apply, replacing mcname with the name of the message channel under which the rule was deleted: