diff --git a/Reconstruction/RecExample/RecExRecoTest/python/CaloReco_RAW_data22_13p6TeV.py b/Reconstruction/RecExample/RecExRecoTest/python/CaloReco_RAW_data22_13p6TeV.py
index 15dc4649aab898fabd21528dc513e4eeaab21cc0..3b465e797120caabc090b7e387011d4310bcc257 100644
--- a/Reconstruction/RecExample/RecExRecoTest/python/CaloReco_RAW_data22_13p6TeV.py
+++ b/Reconstruction/RecExample/RecExRecoTest/python/CaloReco_RAW_data22_13p6TeV.py
@@ -3,11 +3,10 @@
 if __name__=="__main__":
     from AthenaConfiguration.AllConfigFlags import initConfigFlags
     flags = initConfigFlags()
-    # Required for MT using --threads argument
-    flags.fillFromArgs(parser=flags.getArgumentParser())
 
     from RecExRecoTest.RecExReco_setupData22 import RecExReco_setupData22
     RecExReco_setupData22(flags)
+    flags.fillFromArgs()
     flags.lock()
 
     from AthenaConfiguration.MainServicesConfig import MainServicesCfg
diff --git a/Reconstruction/RecExample/RecExRecoTest/python/CaloTopoClusterReco_ESDMC21.py b/Reconstruction/RecExample/RecExRecoTest/python/CaloTopoClusterReco_ESDMC21.py
index 11196fbf4d8dc5ce9ce1d43a8b4a61756fefe45b..3b3dcf400398b5e3ca28bba089c0935e0ebb95b5 100644
--- a/Reconstruction/RecExample/RecExRecoTest/python/CaloTopoClusterReco_ESDMC21.py
+++ b/Reconstruction/RecExample/RecExRecoTest/python/CaloTopoClusterReco_ESDMC21.py
@@ -1,12 +1,12 @@
+#!/usr/bin/env athena.py --CA
 # Copyright (C) 2002-2024 CERN for the benefit of the ATLAS collaboration
 
 if __name__=="__main__":
     from AthenaConfiguration.AllConfigFlags import initConfigFlags
     flags = initConfigFlags()
-    # Required for MT using --threads argument
-    flags.fillFromArgs(parser=flags.getArgumentParser())
 
     flags.Input.Files = ["/cvmfs/atlas-nightlies.cern.ch/repo/data/data-art/RecExRecoTest/mc21_13p6TeV/ESDFiles/mc21_13p6TeV.421450.PhPy8EG_A14_ttbar_hdamp258p75_SingleLep_fct.recon.ESD.e8445_e8447_s3822_r13565/ESD.28877240._000046.pool.root.1"]
+    flags.fillFromArgs()
     flags.lock()
 
     from AthenaConfiguration.MainServicesConfig import MainServicesCfg
diff --git a/Reconstruction/RecExample/RecExRecoTest/python/EGammaReco_RAW_data22_13p6TeV.py b/Reconstruction/RecExample/RecExRecoTest/python/EGammaReco_RAW_data22_13p6TeV.py
index 17afdccfe1ca480d476669dd7b308969d9e50b4d..7c93c4553faaf901f373b4dadb94adba836a5c1c 100644
--- a/Reconstruction/RecExample/RecExRecoTest/python/EGammaReco_RAW_data22_13p6TeV.py
+++ b/Reconstruction/RecExample/RecExRecoTest/python/EGammaReco_RAW_data22_13p6TeV.py
@@ -3,8 +3,6 @@
 if __name__=="__main__":
     from AthenaConfiguration.AllConfigFlags import initConfigFlags
     flags = initConfigFlags()
-    # Required for MT using --threads argument
-    flags.fillFromArgs(parser=flags.getArgumentParser())
 
     from RecExRecoTest.RecExReco_setupData22 import RecExReco_setupData22
     RecExReco_setupData22(flags)
diff --git a/Reconstruction/RecExample/RecExRecoTest/python/Jets_AODMC21.py b/Reconstruction/RecExample/RecExRecoTest/python/Jets_AODMC21.py
index 3a129a82429deefe07051c0edd680657186ab54a..795f6b5cf85b8dddfbc9a6e8a0d37e9760a3925e 100644
--- a/Reconstruction/RecExample/RecExRecoTest/python/Jets_AODMC21.py
+++ b/Reconstruction/RecExample/RecExRecoTest/python/Jets_AODMC21.py
@@ -1,15 +1,15 @@
+#!/usr/bin/env athena.py --CA
 # Copyright (C) 2002-2024 CERN for the benefit of the ATLAS collaboration
 
 if __name__=="__main__":
     from AthenaConfiguration.AllConfigFlags import initConfigFlags
     flags = initConfigFlags()
-    # Required for MT using --threads argument
-    flags.fillFromArgs(parser=flags.getArgumentParser())
 
     flags.Input.Files = ["/cvmfs/atlas-nightlies.cern.ch/repo/data/data-art/RecExRecoTest/mc21_13p6TeV/AODFiles/mc21_13p6TeV.421450.PhPy8EG_A14_ttbar_hdamp258p75_SingleLep_fct.merge.AOD.e8445_e8447_s3822_r13565_r13491/AOD.28775909._000037.pool.root.1"]
     # We have to set the production step, which PFFlow muon linking uses for autoconfiguration.
     from AthenaConfiguration.Enums import ProductionStep
     flags.Common.ProductionStep=ProductionStep.Derivation
+    flags.fillFromArgs()
     flags.lock()
 
     from AthenaConfiguration.MainServicesConfig import MainServicesCfg
diff --git a/Reconstruction/RecExample/RecExRecoTest/python/METReco_ESDMC21.py b/Reconstruction/RecExample/RecExRecoTest/python/METReco_ESDMC21.py
index ba6d83c0219526f50f459bc461d244882de33288..f0c281ab317315199e4efeb9d1bec015002ef665 100644
--- a/Reconstruction/RecExample/RecExRecoTest/python/METReco_ESDMC21.py
+++ b/Reconstruction/RecExample/RecExRecoTest/python/METReco_ESDMC21.py
@@ -1,10 +1,9 @@
+#!/usr/bin/env athena.py --CA
 # Copyright (C) 2002-2024 CERN for the benefit of the ATLAS collaboration
 
 if __name__=="__main__":
     from AthenaConfiguration.AllConfigFlags import initConfigFlags
     flags = initConfigFlags()
-    # Required for MT using --threads argument
-    flags.fillFromArgs(parser=flags.getArgumentParser())
 
     flags.Input.Files = ["/cvmfs/atlas-nightlies.cern.ch/repo/data/data-art/RecExRecoTest/mc21_13p6TeV/ESDFiles/mc21_13p6TeV.421450.PhPy8EG_A14_ttbar_hdamp258p75_SingleLep_fct.recon.ESD.e8445_e8447_s3822_r13565/ESD.28877240._000046.pool.root.1"]
     # Use latest MC21 tag to pick up latest muon folders apparently needed
@@ -12,6 +11,7 @@ if __name__=="__main__":
     # We have to set the production step, which PFFlow muon linking uses for autoconfiguration.
     from AthenaConfiguration.Enums import ProductionStep
     flags.Common.ProductionStep=ProductionStep.Derivation
+    flags.fillFromArgs()
     flags.lock()
 
     from AthenaConfiguration.MainServicesConfig import MainServicesCfg
diff --git a/Reconstruction/RecExample/RecExRecoTest/python/MuonReco_RAW_data22_13p6TeV.py b/Reconstruction/RecExample/RecExRecoTest/python/MuonReco_RAW_data22_13p6TeV.py
index b62fa4860410a399a3c56735feb7c4e9e2e9534c..d461b3ba0c092972edab984e509db07b31b57bdb 100644
--- a/Reconstruction/RecExample/RecExRecoTest/python/MuonReco_RAW_data22_13p6TeV.py
+++ b/Reconstruction/RecExample/RecExRecoTest/python/MuonReco_RAW_data22_13p6TeV.py
@@ -1,13 +1,13 @@
+#!/usr/bin/env athena.py --CA
 # Copyright (C) 2002-2024 CERN for the benefit of the ATLAS collaboration
 
 if __name__=="__main__":
     from AthenaConfiguration.AllConfigFlags import initConfigFlags
     flags = initConfigFlags()
-    # Required for MT using --threads argument
-    flags.fillFromArgs(parser=flags.getArgumentParser())
     
     from RecExRecoTest.RecExReco_setupData22 import RecExReco_setupData22
     RecExReco_setupData22(flags)
+    flags.fillFromArgs()
     flags.lock()
 
     from AthenaConfiguration.MainServicesConfig import MainServicesCfg
diff --git a/Reconstruction/RecExample/RecExRecoTest/python/TauReco_RAW_data22_13p6TeV.py b/Reconstruction/RecExample/RecExRecoTest/python/TauReco_RAW_data22_13p6TeV.py
index fe80d1ce6401c7e1432324afd2252510ef30d951..8ce954866cee835c2dbaaacb192a3a6a49da6272 100644
--- a/Reconstruction/RecExample/RecExRecoTest/python/TauReco_RAW_data22_13p6TeV.py
+++ b/Reconstruction/RecExample/RecExRecoTest/python/TauReco_RAW_data22_13p6TeV.py
@@ -1,10 +1,9 @@
+#!/usr/bin/env athena.py --CA
 # Copyright (C) 2002-2024 CERN for the benefit of the ATLAS collaboration
 
 if __name__=="__main__":
     from AthenaConfiguration.AllConfigFlags import initConfigFlags
     flags = initConfigFlags()
-    # Required for MT using --threads argument
-    flags.fillFromArgs(parser=flags.getArgumentParser())
 
     from RecExRecoTest.RecExReco_setupData22 import RecExReco_setupData22
     RecExReco_setupData22(flags)
@@ -20,6 +19,7 @@ if __name__=="__main__":
     flags.Reco.PostProcessing.GeantTruthThinning = False
     flags.Reco.PostProcessing.TRTAloneThinning = False
 
+    flags.fillFromArgs()
     flags.lock()
 
     from RecJobTransforms.RecoSteering import RecoSteering
diff --git a/Reconstruction/RecExample/RecExRecoTest/python/TrackingReco_ESDMC21.py b/Reconstruction/RecExample/RecExRecoTest/python/TrackingReco_ESDMC21.py
index 22d6a0e49af525790f3c2cfe8f318df1a18b5152..b9928268279dd38d03067d741ce364a818efb8ac 100644
--- a/Reconstruction/RecExample/RecExRecoTest/python/TrackingReco_ESDMC21.py
+++ b/Reconstruction/RecExample/RecExRecoTest/python/TrackingReco_ESDMC21.py
@@ -1,10 +1,9 @@
+#!/usr/bin/env athena.py --CA
 # Copyright (C) 2002-2024 CERN for the benefit of the ATLAS collaboration
 
 if __name__=="__main__":
     from AthenaConfiguration.AllConfigFlags import initConfigFlags
     flags = initConfigFlags()
-    # Required for MT using --threads argument
-    flags.fillFromArgs(parser=flags.getArgumentParser())
 
     flags.Input.Files = ["/cvmfs/atlas-nightlies.cern.ch/repo/data/data-art/RecExRecoTest/mc21_13p6TeV/ESDFiles/mc21_13p6TeV.421450.PhPy8EG_A14_ttbar_hdamp258p75_SingleLep_fct.recon.ESD.e8445_e8447_s3822_r13565/ESD.28877240._000046.pool.root.1"]
     # Use latest MC21 tag to pick up latest muon folders apparently needed
@@ -21,6 +20,7 @@ if __name__=="__main__":
         flags.Tracking.doCaloSeededAmbi=False
         flags.Detector.EnableCalo=False
 
+    flags.fillFromArgs()
     flags.lock()
 
     from AthenaConfiguration.MainServicesConfig import MainServicesCfg
diff --git a/Reconstruction/RecExample/RecExRecoTest/python/TrackingReco_RAW_data22_13p6TeV.py b/Reconstruction/RecExample/RecExRecoTest/python/TrackingReco_RAW_data22_13p6TeV.py
index 3a911d62108248e5c9c5ee21d170395fbc99839d..73c0b132b50e3e626197800e64d0d5c38ae8d43f 100644
--- a/Reconstruction/RecExample/RecExRecoTest/python/TrackingReco_RAW_data22_13p6TeV.py
+++ b/Reconstruction/RecExample/RecExRecoTest/python/TrackingReco_RAW_data22_13p6TeV.py
@@ -1,13 +1,13 @@
+#!/usr/bin/env athena.py --CA
 # Copyright (C) 2002-2024 CERN for the benefit of the ATLAS collaboration
 
 if __name__=="__main__":
     from AthenaConfiguration.AllConfigFlags import initConfigFlags
     flags = initConfigFlags()
-    # Required for MT using --threads argument
-    flags.fillFromArgs(parser=flags.getArgumentParser())
 
     from RecExRecoTest.RecExReco_setupData22 import RecExReco_setupData22
     RecExReco_setupData22(flags)
+    flags.fillFromArgs()
     flags.lock()
 
     from AthenaConfiguration.MainServicesConfig import MainServicesCfg