There are no current rules for changing Faction abilities.
It could fall under the scope of Scenario rules that you create.
As a for instance, in my 4SW campaign, I gave "achievement awards (and penalties)" for specific instances.
Example: if the FS player did three successful MOS7+ Propaganda ops, signifying Operation Galahad, then they received the Superior Counterintelligence Faction Ability.
As long as the FWL player did NOT attack more than 2 worlds a round during the 4SW, they would have the Booming Economy trait. Once they break this, however, they lose the trait.