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If it helps anyone, I have found a satisfying solution, I don't know if it is state of the art, but it achieves my goals.

!- =========== ALL OBJECTS IN CLASS: ENERGYMANAGEMENTSYSTEM:PROGRAMCALLINGMANAGER ===========

EnergyManagementSystem:ProgramCallingManager, WarmupFlagCaller, !- Name AfterNewEnvironmentWarmUpIsComplete, !- EnergyPlus Model Calling Point WarmupFlagProgram; !- Program Name 1

!- =========== ALL OBJECTS IN CLASS: ENERGYMANAGEMENTSYSTEM:PROGRAM ===========

EnergyManagementSystem:Program, WarmupFlagProgram, !- Name SET WarmupFlagProxy = 1; !- Program Line 1

!- =========== ALL OBJECTS IN CLASS: ENERGYMANAGEMENTSYSTEM:GLOBALVARIABLE ===========

EnergyManagementSystem:GlobalVariable, WarmupFlagProxy; !- Erl Variable 1 Name

!- =========== ALL OBJECTS IN CLASS: ENERGYMANAGEMENTSYSTEM:OUTPUTVARIABLE ===========

EnergyManagementSystem:OutputVariable, WarmUpFlagEP, !- Name WarmupFlagProxy, !- EMS Variable Name Averaged, !- Type of Data in Variable ZoneTimestep; !- Update Frequency

!- =========== ALL OBJECTS IN CLASS: EXTERNALINTERFACE:FUNCTIONALMOCKUPUNITIMPORT:FROM:VARIABLE ===========

ExternalInterface:FunctionalMockupUnitImport:From:Variable, EMS, !- Output:Variable Index Key Name WarmUpFlagEP, !- Output:Variable Name agentFMU.fmu, !- FMU File Name FMI, !- FMU Instance Name WarmUpFlag; !- FMU Variable Name

If it helps anyone, I have found a satisfying solution, I don't know if it is state of the art, but it achieves my goals.

!-   ===========  ALL OBJECTS IN CLASS: ENERGYMANAGEMENTSYSTEM:PROGRAMCALLINGMANAGER ===========
 
===========

EnergyManagementSystem:ProgramCallingManager,
    WarmupFlagCaller,        !- Name
    AfterNewEnvironmentWarmUpIsComplete,  !- EnergyPlus Model Calling Point
    WarmupFlagProgram;       !- Program Name 1
 
1


!-   ===========  ALL OBJECTS IN CLASS: ENERGYMANAGEMENTSYSTEM:PROGRAM ===========
 
===========

EnergyManagementSystem:Program,
    WarmupFlagProgram,       !- Name
    SET WarmupFlagProxy = 1; !- Program Line 1
 
1


!-   ===========  ALL OBJECTS IN CLASS: ENERGYMANAGEMENTSYSTEM:GLOBALVARIABLE ===========
 
===========

EnergyManagementSystem:GlobalVariable,
    WarmupFlagProxy;         !- Erl Variable 1 Name
 
Name


!-   ===========  ALL OBJECTS IN CLASS: ENERGYMANAGEMENTSYSTEM:OUTPUTVARIABLE ===========
 
===========

EnergyManagementSystem:OutputVariable,
    WarmUpFlagEP,            !- Name
    WarmupFlagProxy,         !- EMS Variable Name
    Averaged,                !- Type of Data in Variable
    ZoneTimestep;            !- Update Frequency
 
Frequency


!-   ===========  ALL OBJECTS IN CLASS: EXTERNALINTERFACE:FUNCTIONALMOCKUPUNITIMPORT:FROM:VARIABLE ===========
 
===========

ExternalInterface:FunctionalMockupUnitImport:From:Variable,
    EMS,                     !- Output:Variable Index Key Name
    WarmUpFlagEP,            !- Output:Variable Name
    agentFMU.fmu,     !- FMU File Name
    FMI,                     !- FMU Instance Name
    WarmUpFlag;              !- FMU Variable Name
 Name