Minecraft – How to undo killing all entities on a server

The /kill command does not support killing objects (not yet anyway) who fit through a NBT citeria. Only identifiers with the @e command will be considered.

When you entered:

kill @e[type=Item] {Item:{tag:{display:{Name:"RedFlag"}}}
kill @e[type=Item] {Item:{id:"red_flower",Damage:2}}

It is considered as:

kill @e[type=Item]
kill @e[type=Item]

Regardless of how much NBT data an object has, it'll always kill all the entities of the type specified.

This means that /kill @e[type=Sheep] {CustomName:"Sheep"} will kill all sheep(s) in the world. Even if they have/don't have the custom name "Sheep", or a completely different name altogether.
Think about all the sheeps! (Those loaded in anyway)

For servers like Mineplex, they most likely use a plugin, simply because they're more configurable and reliable.

If you want to shut down the server at a specified time, that can be easily done with various pre-existing plugins. From a Google search I found AutoShutdown. This basically shuts down and restarts the server at times you can specify, along with some other features. Just before the server shuts down you can kick all the players to a lobby using, maybe, BungeeTeleporter.

However, if you want to shut the server down when a game ends, that may be more complicated. Doing so would probably require that a specific condition be filled for the game to be counted as over, such as only 1 player left alive, or a timer runs out. I haven't found a plugin for this, but if you're proficient with Java and plugin development it's possible to make your own.

You may also want to reset the world when the game is over to prepare for a new match. I recommend WorldReset to automatically restore from a backup.