I upgraded BI form 1.1.3 to 1.1.4 today and this causes my headless server to refuse to start.

The relevant log entries:

 214.961 Script @__Bio_Industries__/migrations/Bio_Industries_0.18.34_+_1.01.04.lua:1: Entered migration script 1_00_04.lua of "Bio_Industries".
 214.961 Script @__Bio_Industries__/common.lua:76: common.RAIL_BRIDGE_MASK: {
  "object-layer",
  "consider-tile-transitions",
  "rail-layer"
}
 214.961 Script @__Bio_Industries__/common.lua:77: common.RAIL_MASK: {
  "object-layer",
  "consider-tile-transitions",
  "rail-layer",
  "item-layer",
  "water-tile"
}
 215.818 Error ServerMultiplayerManager.cpp:91: MultiplayerManager failed: "Error while applying migration: Bio Industries: Bio_Industries_0.18.34_+_1.01.04.lua

Given entity doesn't exist anymore.
stack traceback:
        [C]: in function 'connect_neighbour'
        __Bio_Industries__/common.lua:486: in function 'connect_power_rail'
        ...stries__/migrations/Bio_Industries_0.18.34_+_1.01.04.lua:57: in function 'add_hidden_entity'
        ...stries__/migrations/Bio_Industries_0.18.34_+_1.01.04.lua:88: in main chunk"
 215.818 Info ServerMultiplayerManager.cpp:780: updateTick(4294967295) changing state from(CreatingGame) to(InitializationFailed)

All but a few pieces of rail on my map are powered rail, there are a few https://mods.factorio.com/mod/railloader stations mixed in though. The rail network also functions as my main power grid, so there are a lot of poles putting in and taking out power from the rails.

Found the debug setting, here's a bit longer excerpt:

 212.168 Script @__Bio_Industries__/common.lua:273: bi-rail-hidden-power-pole (54550) is OK!
 212.168 Script @__Bio_Industries__/common.lua:273: bi-straight-rail-power (54545) is a registered entity. Checking hidden entities: {
  base = {
    __self = "userdata"
  },
  pole = {
    __self = "userdata"
  }
}
 212.168 Script @__Bio_Industries__/common.lua:273: bi-rail-hidden-power-pole (54546) is OK!
 212.168 Script @__Bio_Industries__/common.lua:273: bi-straight-rail-power (54564) is a registered entity. Checking hidden entities: {
  base = {
    __self = "userdata"
  },
  pole = {
    __self = "userdata"
  }
}
 212.168 Script @__Bio_Industries__/common.lua:273: bi-rail-hidden-power-pole (54565) is OK!
 212.168 Script @__Bio_Industries__/common.lua:273: bi-straight-rail-power (54551) is a registered entity. Checking hidden entities: {
  base = {
    __self = "userdata"
  },
  pole = {
    __self = "userdata"
  }
}
 212.168 Script @__Bio_Industries__/common.lua:273: bi-rail-hidden-power-pole (54552) is OK!
 212.168 Script @__Bio_Industries__/common.lua:273: bi-straight-rail-power (54547) is a registered entity. Checking hidden entities: {
  base = {
    __self = "userdata"
  },
  pole = {
    __self = "userdata"
  }
}
 212.168 Script @__Bio_Industries__/common.lua:273: bi-rail-hidden-power-pole (54548) is OK!
 212.169 Script @__Bio_Industries__/common.lua:273: bi-straight-rail-power (54591) is a registered entity. Checking hidden entities: {
  base = {
    __self = "userdata"
  },
  pole = {
    __self = "userdata"
  }
}
 212.169 Script @__Bio_Industries__/common.lua:273: bi-rail-hidden-power-pole (54592) is OK!
 212.169 Script @__Bio_Industries__/common.lua:273: bi-straight-rail-power (54573) is a registered entity. Checking hidden entities: {
  base = {
    __self = "userdata"
  },
  pole = {
    __self = "userdata"
  }
}
 212.169 Script @__Bio_Industries__/common.lua:273: Adding hidden pole to bi-straight-rail-power (54573)
 212.169 Script @__Bio_Industries__/common.lua:273: base.unit_number: 54573
 212.169 Script @__Bio_Industries__/common.lua:273: size of global[tab]: 3600
 212.169 Script @__Bio_Industries__/common.lua:273: #g_table: 3600
 212.169 Script @__Bio_Industries__/common.lua:273: hidden_entity_names: {
  pole = "bi-rail-hidden-power-pole"
}
 212.180 Script @__Bio_Industries__/common.lua:273: g_table[54573]: {
  base = {
    __self = "userdata"
  },
  pole = {
    __self = "userdata"
  }
}
 212.183 Script @__Bio_Industries__/common.lua:273: Removed all wires from bi-rail-hidden-power-pole 244434
 212.183 Script @__Bio_Industries__/common.lua:273: Looking for rails at front
 212.183 Script @__Bio_Industries__/common.lua:273: Looking for rails in left direction
 212.183 Script @__Bio_Industries__/common.lua:273: Rail left of bi-straight-rail-power (54573): nil (nil)
 212.183 Script @__Bio_Industries__/common.lua:273: Looking for rails in straight direction
 212.184 Script @__Bio_Industries__/common.lua:273: Rail straight of bi-straight-rail-power (54573): bi-straight-rail-power (54571)
 212.845 Error ServerMultiplayerManager.cpp:91: MultiplayerManager failed: "Error while applying migration: Bio Industries: Bio_Industries_0.18.34_+_1.01.04.lua

Given entity doesn't exist anymore.
stack traceback:
    [C]: in function 'connect_neighbour'
    __Bio_Industries__/common.lua:486: in function 'connect_power_rail'
    ...stries__/migrations/Bio_Industries_0.18.34_+_1.01.04.lua:57: in function 'add_hidden_entity'
    ...stries__/migrations/Bio_Industries_0.18.34_+_1.01.04.lua:88: in main chunk"
 212.845 Info ServerMultiplayerManager.cpp:780: updateTick(4294967295) changing state from(CreatingGame) to(InitializationFailed)

[EDIT] Sorry, that was too fast -- it's a bit more complicated!

Should be fixed in 0.18.35/1.1.5. Can you confirm that?

1.1.5 doesn't even get to the migrations, instead it fails loading with

174.076 Error ModManager.cpp:1560: Error while running setup for entity prototype "bi-bio-farm-hidden-panel" (solar-panel): next_upgrade can't be set when flag 'not-upgradable' is set.

Please provide a saved game! I don't get the error with or without Mining Drones/Transport Drones (both modify our compound entities), neither with nor without my debugging mod. But it's really weird that so many people report the same bug.

The crash on starting should be fixed in 1.1.6.

1.1.6 Starts up fine and loads my save without errors.

Nice! :-)