When a player tries to build an entity at where is another team's start zone (and the start zone protection is enabled), the server crashes with following logs:

42587.621 Error MainLoop.cpp:1029: Exception at tick 7343559: Error while running event level::on_built_entity (ID 6)
LuaEntity API call when LuaEntity was invalid.
stack traceback:
...io/temp/currently-playing/addons/Diplomacy/functions.lua:45: in function 'protection_from_theft_of_electricity'
/opt/factorio/temp/currently-playing/addons/control.lua:185: in function 'on_built_entity'
/opt/factorio/temp/currently-playing/control.lua:94: in function </opt/factorio/temp/currently-playing/control.lua:92>
42587.621 Error ServerMultiplayerManager.cpp:96: MultiplayerManager failed: "Error while running event level::on_built_entity (ID 6)
LuaEntity API call when LuaEntity was invalid.
stack traceback:
...io/temp/currently-playing/addons/Diplomacy/functions.lua:45: in function 'protection_from_theft_of_electricity'
/opt/factorio/temp/currently-playing/addons/control.lua:185: in function 'on_built_entity'
/opt/factorio/temp/currently-playing/control.lua:94: in function </opt/factorio/temp/currently-playing/control.lua:92>"
42587.621 Info ServerMultiplayerManager.cpp:698: mapTick(7343559) changing state from(InGame) to(Failed)
42587.622 Info GlobalContext.cpp:694: Waiting for child processes to exit:
42587.806 Info ServerMultiplayerManager.cpp:142: Quitting multiplayer connection.
42587.806 Info ServerMultiplayerManager.cpp:698: mapTick(4294967295) changing state from(Failed) to(Closed)
42587.819 Info UDPSocket.cpp:206: Closing socket
42587.819 Info UDPSocket.cpp:236: Socket closed
42587.820 Goodbye

Edit: Sorry for forgetting to set the label of this thread to "bug"

In an nine hours I am will fixing.

And just a small suggestion about start zone: Forbid the biters to enter/migrate to start zones. There're some annoying nests in one of the start zones of an empty team in my server, making it the start zone of biters. You cannot get rid of them unless using the artillery which is disabled in PvP Scenario by default.

Fixed in 1.3.6

You can update the save

1) Need to find path to save (wiki)
p.s. for me: "%appdata%\Factorio\saves"
2) Backup the save (because something can goes wrong)
3) Download the new version of the mod

Variant A (simply, but not working always)

A.1) Go to the folder "...\pack-scenarios_1.3.6\scenarios"
A.2) Pick scenario and open him, example: "pvp(modified)"
A.3) Copy all files from "pvp(modified)", then replace all files in the save

Variant B

B.1) Delete all files in the save except "level.dat", "level-init.dat", "preview.png", "script.dat", "replay.dat", "blueprint.dat" and "info.json" (I hope you understand that all important files is *.dat Do not worry if there are not some)
B.2) Go to the folder "...\pack-scenarios_1.3.6\scenarios"
B.3) Pick scenario and open him, example: "pvp(modified)"
B.4) Copy all files from "pvp(modified)" and paste all files in the save

If there are problems in the game, it can sometimes help to write in chat: "/c game.reload_script()"

If you want to enable "Prohibition spawn biters in starting zone" in the new version of the already started game, then write in chat: "/c global.game_config.prohibition_spawn_biters_in_starting_zone=true"