I tried numerous times to add the winglets manually and using the ACE and somehow managed to see the winglets on it in the preview (selecting details for it in the aircraft selection menu), but in FSX, they were not there. I also noticed that the ACE adds the line wglets=1 to the aircraft.cfg for the 727-200F:

[fltsim.2]
title=CS 727-200F Captain Paint2
sim=cs727200
model=f
panel=
sound=
texture=N905AJ
kb_checklists=
kb_reference=
atc_id=N905AJ
atc_airline=Amerijet International
atc_flight_number=N905AJ
ui_manufacturer=Boeing
ui_type=727-200 another company Freighter
ui_variation=Amerijet N905AJ, 2009 NP
ui_typerole=Commercial Airliner
ui_createdby=Nath2889
visual_damage=1
ui_wglts=1
description="727 Captain: 727-200 ADDON Pack v2.4\n(c) 2011 Captain Sim www.captainsim.com Amerijet International 905. \n Repaint by NATH2889.\n"

but I still don't see them. I tried running the ACE using the "Run as administrator" option, but the winglets still don't show. Interestingly enough, adding winglets to the 727-100F another company and 727-100F another company/RE works fine. Beats me why it won't hold in the 727-200F another company. :(

My advice would be to make sure that the ui_wglts=1 IS present in the 727-200F aircraft.cfg, and maybe one day they will suddenly decide to appear and stay there fr you. :-/