Unless it's Alaska, where nobody would think twice about electing a third-party candidate to the Senate. Montana and Maine would also be dark horse candidates for this kind of thing.
Maine they'd actually be favored, because of IRV (assuming it's upheld). I imagine the Libertarian keeps the major parties below 50%, and would probably get enough #2 votes to win.
They'd potentially lose their committee assignments, but they'd probably remain caucusing with their former party unless they wanted to be completely powerless.
If they continued to caucus with their former party (probably Republican, I can't think of any Democrats who are libertarian-leaning, left-libertarianism is basically a type of liberalism falsely branded as something it's not), they'd probably keep committee assignments (without them they're almost totally useless), but Ryan/McConnell could take retaliatory action.