The beam design rules stored in a project and displayed in the "Design Properties and Rules" menu do not have any influence over the behavior of beam calculations unless they are manually applied to specific elements by the user. Once a design rule has been applied to a beam, the rule will be detected automatically during subsequent calculation launches for that element. The calculation will then load in the ENERCALC interface with the design properties specified by the design rule already applied.
Rules are applied using the "Apply Definition To Elements" button:

When a definition is selected in the table, clicking the "Apply" button will trigger a multi-select process in the Revit UI. EFR will await element selection by the user:


When navigating the Revit UI during the selection process, only beam and girder elements (of all materials) are eligible for selection to apply beam design rules:

When the desired elements have been selected, clicking the "Finish" button will cause the menu table to update with the quantity of elements to which the definition has been applied:

Clicking "Cancel" during the selection process will halt the operation with no impact to the Revit model or the menu table.
Clicking the "Apply" button will have no effect when there is no definition selected in the table:

Clicking the "Apply" button when the currently selected definition contains unsaved changes will result in the following warning:

For more information about "Saved" vs "Unsaved" definitions, refer to Modifying Rules and Adding New Rules.