What happened with your skimmer? Doesn't it flow back to your sump? That really sounds like a mess, sorry to hear it. Are you sure everything died? Much of the corals in nature go through low tide daily, you might be able to salvage them in a QT if you try.
I would say the same thing about the LR. Some things may die but others won't and in time your reef will repair itself as if it were dry rock. Just clean off the obvious dead material so you limit the ammonia spike and call the carpet cleaner.
I think your floor will be the biggest mess to fix.
Good luck,
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