Yes you do. The default airport list is the default list and will never change. However, unless you do 'Find/Collect Airports' and select the 'scenery library' option then none of your active addons or waypoints will be known to AIFP.
In the case of a corruption you can replace the defaults by just copying over the latest AIFP release and replace the addon scenery list by rebuilding it.
If you have never build the addon list before then you will never be able to access an awful lot of bases/waypoints.
To give you example my FS9 AirportList.dat (defaults) is 2,936KB my AirportList_AddOns.dat (addons) is 2215KB. That is a lot of extra places to go to.