Johnson appeared on the GOP ballot here in South Carolina (losing to Cain Colbert among others) and we have a sore loser law that keeps the loser of one party's primary from appearing on the general election ballot, even as the nominee of another party. Not certain if that law applies to Presidential candidates, but if it did, the Libertarians would have to place another name in place of his here.
Sore loser laws typically do not apply to presidential candidates, so that concern, at least, is probably irrelevant.
This is mostly true, but there still at least a couple of states whose sore loser laws as written seem to apply to presidential candidates. There's good precedent to indicate that such laws wouldn't hold up if challenged in court, but that would require money that the Libertarian party probably doesn't have.
