Lot's info requested here! Let's start with Lee's Readme file, Section 12.:
"To restore a stock airport or remove a new airport, simply remove the .bgl file for that airport from the FS Addon Scenery folder
( .../FS9/Addon Scenery/Scenery/ ). If it is a new airport then the airport may continue to be displayed on the Flight Simulator Go To Airport window however, so to eliminate that residual airport listing just call up the Scenery Library window from the FS Settings, and click the OK button to close the window."
this is the folder specified by Lee Swordy who created TTools and AFCAD:
FS9/Addon Scenery/Scenery/
This is where the AF2 files reside for default FS9 installation.
Of course, they can be elsewhere; i.e., in the FS9/Addon Scenery/Scenery/ Subfolder you alluded to. They will all work but DO NOT have duplicates!
How you lost your FS9/Addon Scenery/Scenery/ is beyond me. If this is the case, logic would dictate your FS9 AF2 files are gone as well. I cannot speak to this.
Here's a screen shot of the files in my FS9/Addon Scenery/Scenery/ :
bill
p.s. the F1UTxxx.bgl file are my Flight1 Ultimate Traffic AF2, BGLs