Did All the Flayed Die Stranger Things?

They all stay dead. It's not like they were alive after they were exploded so they could be absorbed into the Mind Flayer. It could be that even if the thing was killed or cut off to the Upside Down before they were absorbed that they were still beyond saving.

Did the flayed die Stranger Things?

It is likely that a total of 30 Hawkins residents (including the aforementioned above minus Will and the rats) were flayed and died as a result of the Mind Flayer's Avatar's death, since it was mentioned by the news in "The Battle of Starcourt" that 30 people died in Starcourt Mall's fire, which was obviously a cover ...

Does Jonathan get flayed?

They hide in a room to call for help, but the clerk is too busy gossiping to pick up, so Bruce reaches them and brutally beats Jonathan until Nancy stabs him in the back and retreats, Bruce again following Nancy while Tom comes for Jonathan, continuing to beat him until Jonathan lies prone on the floor.