There are no default 'AFCAD' files as such. The word 'AFCAD' has come to mean any airport data file, but really should only be applied to the files created by the AFCAD program to modify airports.
The default airport and facility data (AFD) are contained in larger scenery files (.bgl) that contain all the default airports in a given area. The files are 'AP######.bgl' files, found in the various ...\Scenery\
\scenery\.. folders.
Do not do anything to these files, except to open it in AFCAD when you first begin a project to modify an airport. (Sections 9 and 10 in the AFCAD help file-Readme.htm-can explain in further detail.)
When you create and save an AFCAD file to modify an airport, it will automatically over ride the default airport data (listed as STOCK in the AFCAD search results).
You should make sure that there is no more than 1 AFCAD modified airport file (listed as MOD in the AFCAD search results) for any airport, as more than 1 MOD can cause unexpected results.
Dave
At that time [1909] the chief engineer was almost always the chief test pilot as well. That had the fortunate result of eliminating poor engineering early in aviation.