private CompoundCommand deleteFeatureSelection(AssociationEnd associationEnd, EditingDomain editingDomain) {
    CompoundCommand compoundCommand = new CompoundCommand();
    
    //When this is just an append, it works nicely but I need it to be executed before createFeatureSelection
   compoundCommand.appendAndExecute(RemoveCommand.create(editingDomain, associationEnd.getFeatureSelection()));
    return compoundCommand;
}

public void doSomething(AssociationEnd associationEnd) {
    EditingDomain editingDomain = EMFEditUtil.getEditingDomain(associationEnd);
    CompoundCommand compoundCommand = new CompoundCommand();

    compoundCommand.append(deleteFeatureSelection(associationEnd, editingDomain));
    
    //This createFeatureSelection needs all command from deleteFeatureSelection to have been executed
    compoundCommand.append(createFeatureSelection(associationEnd, editingDomain));

    compoundCommand.execute();
}