I'd totally call this a “significant and exceptional” circumstance. I strongly feel that this is exactly the situation in which you can (should??) deviate from… well, don't know where to deviate from, in first place :)

I would ask the player how many cards has his sideboard and if he can remember all of it. I'll grab his decklist for confirmation, and if nothing shady is going on, I'd take the top 13 + bottom 2 as his SB. After that, he can resolve Aetherworks ability.

However, I'm more reluctant about letting previously the scry 2 again from Glassblower. I think a bit of information has been gained from the fact it resolved, and thus may affect the choice for the Aetherworks ability.