I deleted the ones from TrafficX for the sceneries, and that is how I found out that the AFX files were missing.
Just check that you deleted only the files from Traffic X and not the ones coming from our scenery. I'm not sure what you are saying with "AFX files missing". We certainly haven't missed any file, if you just install the scenery with its own installer.
Note that, there's no such thing as an "AFX file". They are all .BGL files, and a .BGL that contains Airport data like parking spots, is commonly known as an AFCAD, which is not an entirely correct term, since it's the name of the most popular utility to open them. In any case, how the file is named is entirely irrelevant, it's the content that matters. We named the AFCAD for PHNL "AP_PHNL.BGL" in FSX and "AF9_PHNL.BGL" in FS9, others named it AFX_xxxxx.BGL, perhaps to indicate they were made with the AFX program, but that's it, you shouldn't assume an AFX file is missing, just because you don't see anything named AFX...
The only traffic.bgl files I see are located in Scenery/world/scenery, and they do not include the airports I have issues with. Should I look somewhere else?
The traffic.bgl file doesn't "include" a specific airport: it's the *schedule* database, that tells which airplane goes from A to B, at which times of the day and/or days of the week.
I've asked you to check if you had multiple traffic.bgl files, and it seems so, considering you used the plural term. Depending how they are made, there might be problems with disappearing traffic, if you have duplicate traffic.bgl files, I think this happens if there's a mix between FSX-native and FS9 versions under FSX, but I'm not 100% sure.
In any case, try to use a single traffic.bgl file, which should be the one that comes with the AI traffic package you use (My Traffic ?), since you need that file, in order to reference the addons AI models, otherwise the default traffic.bgl will only call default traffic.