I've done a similar thing recently with my UK airbases, I've created different versions of the same runway [say runway1] in the types ini and given them small, medium and large targettype entries, that way I can change the active years of a base and its changing role over the years....eg, large runway entry [and inis etc] for bomber operations, then a few years later the same airfield is using the same runway but using the small entry and inis for parking etc for fighter operations.
You need to have your aircraft "MinBaseSize=XXX" entries set up to match the base sizes you would like them to operate from, it's not perfect but most of the time things work as they should.