I'm not sure. When I ran your script with the test table. Both graphs are the same, and both can be exported to PDF. In all 4 (?) cases the local data filter is included with the figures.
 
I messed around with your script a little.
I wrapped the two graphs and the filters in an expression.
When I make the window, I put them directly into the window vlistbox (Lub) by evaluating the expressions there.
 
Then I prepended (opposite of append, kind of) the text to the top.
After the window was complete I journaled it as the last step.  Journals can be a pain to work with so I always try to journal last. Saved the journal as a PDF and then opened it to check to see how it looked. 
 
//*************************************
//dt_source = Data Table( "Wafer_Sort" );
dt_source = Open( "test.jmp" );
set = Expr(
	cht_uNV_EC_RD_Set_AfterCyc = dt_source << Graph Builder(
		Size( 1029, 643 ),
		Show Control Panel( 0 ),
		Variables(
			X( :SplitGrp ),
			X( :Wafer, Position( 1 ) ),
			Y( :Name( "DL_uNV_EC_RD_Set_AfterCyc-DL_uNV_EC_RD_Set_AfterCyc,11510,-" ) )
		),
		Elements( Points( X( 1 ), X( 2 ), Y, Legend( 32 ) ) ), 
	
	
		SendToReport(
			Dispatch(
				{},
				"400",
				LegendBox,
				{Legend Position( {32, [-1]} ), Position( {-1} )}
			)
		)
	)
);
erase = Expr(
	cht_uNV_EC_RD_Erase_AfterCyc = dt_source << Graph Builder(
		Size( 1029, 643 ),
		Show Control Panel( 0 ),
		Variables(
			X( :SplitGrp ),
			X( :Wafer, Position( 1 ) ),
			Y( :Name( "DL_uNV_EC_RD_Erase_AfterCyc-DL_uNV_EC_RD_Erase_AfterCyc,11512,-" ) )
		),
		Elements( Points( X( 1 ), X( 2 ), Y, Legend( 32 ) ) ), 
	
		SendToReport(
			Dispatch(
				{},
				"400",
				LegendBox,
				{Legend Position( {32, [-1]} ), Position( {-1} )}
			)
		)
	)
);
filters = Expr(
	cht_uNV_EC_RD_Set_AfterCyc << Local Data Filter(
		Add Filter(
			columns(
				:Name( "DL_uNV_EC_Set_PreCyc-DL_uNV_EC_Set_PreCyc,11504,-" ),
				:Name( "DL_uNV_EC_RD_Set_PreCyc-DL_uNV_EC_RD_Set_PreCyc,11505,-" ),
				:Name( "DL_uNV_EC_Erase_PreCyc-DL_uNV_EC_Erase_PreCyc,11506,-" ),
				:Name( "DL_uNV_EC_RD_Erase_PreCyc-DL_uNV_EC_RD_Erase_PreCyc,11507,-" ),
				:Name( "DL_uNV_EC_10k_Cycle-DL_uNV_EC_10k_Cycle,11508,-" )
			),
			Where( :Name( "DL_uNV_EC_Set_PreCyc-DL_uNV_EC_Set_PreCyc,11504,-" ) == 0 ),
			Where( :Name( "DL_uNV_EC_RD_Set_PreCyc-DL_uNV_EC_RD_Set_PreCyc,11505,-" ) == 0 ),
			Where( :Name( "DL_uNV_EC_Erase_PreCyc-DL_uNV_EC_Erase_PreCyc,11506,-" ) == 0 ),
			Where(
				:Name( "DL_uNV_EC_RD_Erase_PreCyc-DL_uNV_EC_RD_Erase_PreCyc,11507,-" ) == 0
			),
			Where( :Name( "DL_uNV_EC_10k_Cycle-DL_uNV_EC_10k_Cycle,11508,-" ) == 0 )
		)
	);
	cht_uNV_EC_RD_Erase_AfterCyc << Local Data Filter(
		Add Filter(
			columns(
				:Name( "DL_uNV_EC_Set_PreCyc-DL_uNV_EC_Set_PreCyc,11504,-" ),
				:Name( "DL_uNV_EC_RD_Set_PreCyc-DL_uNV_EC_RD_Set_PreCyc,11505,-" ),
				:Name( "DL_uNV_EC_Erase_PreCyc-DL_uNV_EC_Erase_PreCyc,11506,-" ),
				:Name( "DL_uNV_EC_RD_Erase_PreCyc-DL_uNV_EC_RD_Erase_PreCyc,11507,-" ),
				:Name( "DL_uNV_EC_10k_Cycle-DL_uNV_EC_10k_Cycle,11508,-" )
			),
			Where( :Name( "DL_uNV_EC_Set_PreCyc-DL_uNV_EC_Set_PreCyc,11504,-" ) == 0 ),
			Where( :Name( "DL_uNV_EC_RD_Set_PreCyc-DL_uNV_EC_RD_Set_PreCyc,11505,-" ) == 0 ),
			Where( :Name( "DL_uNV_EC_Erase_PreCyc-DL_uNV_EC_Erase_PreCyc,11506,-" ) == 0 ),
			Where(
				:Name( "DL_uNV_EC_RD_Erase_PreCyc-DL_uNV_EC_RD_Erase_PreCyc,11507,-" ) == 0
			),
			Where( :Name( "DL_uNV_EC_10k_Cycle-DL_uNV_EC_10k_Cycle,11508,-" ) == 0 )
		)
	);
);
nw = New Window( "Reports",
	hlb = H List Box(
		lub = vlist Box( set,erase )
	)
);
filters;
lub << prepend( tb = Text Box( "uNV RD_Set & RD_Erase after 10k
" ));
tb << Set Font Size( 14 ) << Set Font Style( "Bold" ) << Justify Text( "center" );
tb << set width(700) << set wrap(700);
nw<<journal;
//**** Report *******
Reports = Current Journal();
//Reports << Set page setup( margins( 0.1, 0.1, 0.1, 0.1 ), scale( 0.8 ), portrait( 0 ), paper size( "A4" ) );
Reports << Set page setup( margins( 0.05, 0.05, 0.05, 0.05 ), scale( 1 ), portrait( 0 ), paper size( "A3" ) );
Reports << get page setup();
Reports << SavePDF("debug.pdf");
open ("debug.pdf");
//Close All( Data Tables, NoSave );
Close All( Journals, NoSave );
//Exit();
 

 
					
				
			
			
				
	JMP Systems Engineer, Health and Life Sciences (Pharma)