The most innocuous thing will keep this from ever happening. The setting for the final battle. Marvel has a go-to in New York, NY. DC has Gotham City, Coast City, Central City, Star City, Metropolis, Bludhaven, blah blah blah. Just picking the right fake city for the denoument will cause fights that will shelve the stupid thing..
Honestly, I can't see Warner letting such a silly little issue scupper a major production. Just set the thing all over the world, and have Darkseid (or whomever) attacking London, Paris, New York, and Washington D.C. Or maybe set the big finale on the moon or Apokolips.
Nobody but hardcore fanboys will care if the Flash suddenly shows up in Metropolis instead of Central City. And it's not like Warner or DC has a vested interest in promoting the "Star City" brand . . . .