I'm not 100% sure on this so backup the files so you can change it back if needed. But Open each aircrafts folder under DATA/AIR and replace the file that ends in (Aircraft_Name)shp.dds. As long as your not playing with the map contacts off option it should put the little airplane symbol back on the map. the Same works for Ships in the DATA/SEA Ships name folder.
You will probably need a stock install to grab the files from and you will have to add the file for the non-stock ships, its a long process so i would create a test mission to make sure it works before doing all the aircraft. Its a PITA, but i like having contacts and i'm currently doing this in Operation Monsun.
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