You know, editors like ADE are a great advancement, but they introduce extra problems as well. You used to have one location for approach data, Scenery/Generic/scenery, and always separate files for that data. Now that ADE can edit approaches as well, the technical limitation of separate location and file is gone, but put two files at the same layer both with delete statemements and approach data and you're asking for trouble.
For example, with FS9 KTPA, you have the following, from low to high priority:
Stock info contained in AP925220.BGL
Addon Afcad: KTPA_ADE9_ADE.bgl (with deleteAllApproaches="TRUE" (and the others) and a repeat of stock approach info!!!)
Addon approach file: KTPA_approach_fs9.bgl (with deleteAllApproaches="TRUE", which you'd expect, but also delete statemements for everything else, which is odd as the file only contains approach info, but updated this time)
Change the file names and you may very well be reversing the priority of the last two! (Think alphabetical...) Resulting in old approach info overriding new approach info, which in turn overrode the old...
My situation is:
KTPA ADE Approach.bgl (in Scenery/Generic/scenery and with only deleteAllApproaches set and updated approach info)
AF2_KTPA.bgl (in KTPA's scenery folder, no deleteAllApproaches set and no approach info in the file, only other delete statements and your regular Afcad data)
Works like a charm and the Afcad can be (renamed and) edited with any editor including AFCAD, without distroying anything important. Which cannot always be said about files created with later editors and especially ADE...
Anyway, just some background info. May work slightly differently in FSX.