I think the player's coordinates are saved in their own file, rather than the world's, but I can test it real quick.
EDIT: Yup, player position is saved in it's own file. The only thing that needs be deleted is the overworlds region file, which basically only contains block data. Even if it weren't like this, deleting it couldn't impact the players if they were in the nether, since that's a different region file. Level.dat can also be deleted if a new seed is preferred, but I don't think that'll be nessecary, since the new biome generation will probably make the same seed look very different.