Question about NAVAID editing

I'm trying to get the VOR/DME navaids in Thailand, Laos, and South Vietnam to match the historically correct TACAN channels that were used between 1966 to 1973.

I have been able to use ADE to successfully edit navaids that are in add-on scenery ....but am having a problem with navaids in the stock airports.
When I compile and save the stock airports in order to edit them, they lose their navaids. When I add the the corrected navaids and re-compile the airports to the add-on scenery folder, I either end up with an unchanged navaid or I get the old navaid right next to the new one.
It was my understanding that add-on scenery overrides the stock scenery....but it doesn't seem to be the case.
Is there something I need to do to get the new scenery override to stock scenery?

Any ORBX scenery - apart from FTX?
I have found with ADE that ORBX airports are layered strangely and reference files away from the .BGL

No ORBX.
It's stock FSX scenery with FSX@War and FSX@War Southeast Asia theater scenery.
The FSX@War scenery that I edit is being put in another scenery folder that I named FSX@War Pack SEA_Scenario.

My top down hierarchy within Addon Scenery is:

FSX@War Pack SEA_Scenario
FSX@War Pack SEA_Scenario_Generic
FSX@War Pack Southeast Asia
FSX@War Pack Southeast Asia_Generic
FSXatWarPack1
FSXatWarPack1_Generic

I have been able to successfully edit navaid frequency and range as long as it's within the FSX@War Pack Southeast Asia folder. When I compile and save it into the FSX@War Pack SEA_Scenario folder it overrides the scenery in the original folder (FSX@War Pack Southeast Asia) and shows up in FSX exactly the way I want it to. I have also been able to add a new navaid for Skyline Ridge (near LS-20A Long Tieng).

The problem I'm facing is that the ones I still need to change (U-Tapao, Korat, Udorn, Don Maung (BKK), Hue/Phu Bai, Ubon, Da Nang, Pakse, Phu Cat, NKP and Savanaket) are all using stock navaids.

When I use ADE to pull them from the stock airports list, I compile and save them to the FSX@War Pack SEA_Scenario folder.
The navaids that showed up in these airports don't come over when I do this though....so I have to add the navaid into it and save it.
When I then check it in FSX, I end up with both the original navaid from the stock airport and the new navaid I created.

I have since found out that my problem is due to a limitation within FSX that prevents stock navaids from being excluded by addon scenery.