The solution is NOT to let athletes run both, but rather COMBINE them.
It's DUMB to have 2 different national championships, it would be dumb to have the same kids race each other for a 2nd time but on a different course, it's dumb to keep the kids away from school for so long to race 2 championships, and it's dumb to over-race them and burn them out as high schoolers.
If it's Foot Locker sponsored by Hoka this year, why can't it eventually be Foot Locker sponsored by Nike? Forget the history of the old course, put it on a course big enough to host 300+ runners per gender. The excitement of a new page will far outweigh the loss of the historical aspect, but new history will be created.
An added benefit to both Nike and Footlocker is that they can split the cost - and the extra hype may help them both to turn a big profit off the meet.