If it's OK to create a new graph, you can work with the script, replace the Where() expression with a new on and then evaluate the new code:
Names Default To Here( 1 );
dt = Open( "$SAMPLE_DATA/Big Class.jmp" );
gb = dt << Graph Builder(
Variables( X( :weight ), Y( :height ), Color( :sex ) ),
Elements( Points( X, Y, Legend( 3 ) ) ),
Where( :sex == "F" )
);
script = gb << get script;
whereexpr= extract expr(script, Where(wildList()));
Substitute into (script, Name Expr(where expr), Expr(___W___));
// later:
new whereexpr = Expr(Where( :sex == "M" ));
Substitute into (script, Expr(___W___) , Name Expr(new whereexpr));
Eval(script)