Dillon, if you use ActiveSky, you could disable automatic updates, so you know what the weather will be like at the destination airport. That'll allow you to activate the proper Afcad. I only use one Afcad for KORD, but at several airports, I use two or even three. Especially at airports with one-way runways. Although not entirely realistic, KORD can work well without the need for multiple Afcads. My set-up uses three take-off and three landing runways at all times. Same as with the old SF scenery. I have a flight planned from KIAD to KORD in a United 763, should be sweet.
Harpsi, if you want a runway x/y to become y/x, you shouldn't need to tinker with ILS info. Unless the info was changed from the stock info. I have done this "runway flipping" at several airports and I've developed a fail-safe routine. Display Navaids, try and delete a navaid for a runway end, if available. If it tells you stock info can't be deleted, fine. If It "deletes" user modications and reverts back to stock settings, undo, then screen capture the properties of that navaid for later reference. Do this for both ends.
Then capture the properties of the runway in question. Then delete the runway. Then re-insert it, but "flip" all info. So if the base end was x, make the new base y, do this for all info. Markings, lights if applicable, etc... After you've re-inserted the runway, the navaids should already be linked to the proper ends. If you had to capture any ILS info, go into the properties of that ILS and make changes to reflect that capture. After that, the runway will be exactly the same and fully functional, except that the reciprocal end is now the base end.
It sounds like a lot of work, but as you know, it can be very helpful to recreate certain runway configurations.