Bit of a problem for Red Bull (the heart bleeds for them, they're so good for football); Salzburg and Leipzig are both going to qualify for the Champions League. But Leipzig - who clearly have priority within the group now - will almost certainly end up finishing lower in their respective league table and so under UEFA rules which prohibit clubs under the same ownership from participating in the same competition, they'll be the ones to miss out.
Not sure if they'll get demoted to the Europa League or just flat out banned from European competition (in fact they probably will have to be blocked because Salzburg could get to the group stage, finish 3rd and drop into the EL...whereby you have the same problem should Leipzig qualify from their EL group)