diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3c1844435e..bcfe63e72c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,4 +1,5 @@
 
+
 # Changelog
 All notable changes to this project will be documented in this file.
 
@@ -11,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Add Key-Value store for instance settings
 - Allow for Re-extractions of projects to a database, see [ExecuteFullExtractionToDatabaseMSSql](Documentation\DataExtractions\ExecuteFullExtractionToDatabaseMSSql.md)
+- When cloning an ExtractionConfiguration with a deprecated catalogue, the GUI will ask if you want to replace the deprecated catalogue with the known replacement
 - Add ability to customise LoadMetdata Folder Location. See [LoadMetadata](Documentation\DataLoadEngine\LoadMetadata.md)
 - Add ability to point a catalogue to a new data source [Documentation](./Documentation/Catalogues/UpdateCatalogueDataLocation.md)
 - Allow DQE graphs to be scrollable and scalable
diff --git a/Rdmp.Core/CommandExecution/AtomicCommands/ExecuteCommandCloneExtractionConfiguration.cs b/Rdmp.Core/CommandExecution/AtomicCommands/ExecuteCommandCloneExtractionConfiguration.cs
index 5715ae412a..2fcb3707f1 100644
--- a/Rdmp.Core/CommandExecution/AtomicCommands/ExecuteCommandCloneExtractionConfiguration.cs
+++ b/Rdmp.Core/CommandExecution/AtomicCommands/ExecuteCommandCloneExtractionConfiguration.cs
@@ -1,9 +1,11 @@
-// Copyright (c) The University of Dundee 2018-2019
+// Copyright (c) The University of Dundee 2018-2024
 // This file is part of the Research Data Management Platform (RDMP).
 // RDMP is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
 // RDMP is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
 // You should have received a copy of the GNU General Public License along with RDMP. If not, see <https://www.gnu.org/licenses/>.
 
+using System;
+using System.Collections.Generic;
 using System.Linq;
 using Rdmp.Core.Curation.Data;
 using Rdmp.Core.DataExport.Data;
@@ -17,12 +19,53 @@ namespace Rdmp.Core.CommandExecution.AtomicCommands;
 public class ExecuteCommandCloneExtractionConfiguration : BasicCommandExecution, IAtomicCommand
 {
     private readonly ExtractionConfiguration _extractionConfiguration;
+    private readonly IBasicActivateItems _activeItems;
+    private readonly List<IExtractableDataSet> toRemove = [];
+    private readonly List<Catalogue> toAdd = [];
+    private void CheckForDeprecatedCatalogues()
+    {
+        if (_extractionConfiguration.SelectedDataSets.Any(sd => sd.GetCatalogue().IsDeprecated) && _activeItems.IsInteractive)
+        {
+            if (YesNo("There are Deprecated catalogues in this Extraction Configuration. Would you like to replace them with their replacement (where available)?", "Replace Deprecated Catalogues"))
+            {
+                var repo = _activeItems.RepositoryLocator.CatalogueRepository;
+                var DeprecatedDatasets = _extractionConfiguration.SelectedDataSets.Where(sd => sd.GetCatalogue().IsDeprecated).ToList();
+                var replacedBy = repo.GetExtendedProperties(ExtendedProperty.ReplacedBy);
+                foreach (ISelectedDataSets ds in DeprecatedDatasets)
+                {
+                    var replacement = replacedBy.Where(rb => rb.ReferencedObjectID == ds.GetCatalogue().ID).FirstOrDefault();
+                    if (replacement is not null)
+                    {
+                        var replacementCatalogue = repo.GetObjectByID<Catalogue>(Int32.Parse(replacement.Value));
+                        while (replacementCatalogue.IsDeprecated)
+                        {
+                            var replacementCatalogueIsReplacedBy = replacedBy.Where(rb => rb.ReferencedObjectID == replacementCatalogue.ID).FirstOrDefault();
+                            if(replacementCatalogueIsReplacedBy is not null)
+                            {
+                                //have found further down the tree
+                                replacementCatalogue = repo.GetObjectByID<Catalogue>(Int32.Parse(replacementCatalogueIsReplacedBy.Value));
+                            }
+                            else
+                            {
+                                //there is no replacement
+                                break;
+                            }
+                        }
+                        toRemove.Add(ds.ExtractableDataSet);
+                        toAdd.Add(replacementCatalogue);
+                    }
+                }
+
+
+            }
+        }
+    }
 
     public ExecuteCommandCloneExtractionConfiguration(IBasicActivateItems activator,
         ExtractionConfiguration extractionConfiguration) : base(activator)
     {
         _extractionConfiguration = extractionConfiguration;
-
+        _activeItems = activator;
         if (!_extractionConfiguration.SelectedDataSets.Any())
             SetImpossible("ExtractionConfiguration does not have any selected datasets");
     }
@@ -36,9 +79,24 @@ public override Image<Rgba32> GetImage(IIconProvider iconProvider) =>
     public override void Execute()
     {
         base.Execute();
+        CheckForDeprecatedCatalogues();
 
         var clone = _extractionConfiguration.DeepCloneWithNewIDs();
-
+        foreach (ExtractableDataSet ds in toRemove)
+        {
+            clone.RemoveDatasetFromConfiguration(ds);
+        }
+        foreach (Catalogue c in toAdd)
+        {
+            //check if the eds already exis
+            var eds = _activeItems.RepositoryLocator.DataExportRepository.GetAllObjectsWhere<ExtractableDataSet>("Catalogue_ID", c.ID).FirstOrDefault();
+            if (eds is null)
+            {
+                eds = new ExtractableDataSet(_activeItems.RepositoryLocator.DataExportRepository, c);
+                eds.SaveToDatabase();
+            }
+            clone.AddDatasetToConfiguration(eds);
+        }
         Publish((DatabaseEntity)clone.Project);
         Emphasise(clone);
     }
diff --git a/Rdmp.Core/CommandExecution/AtomicCommands/ExecuteCommandDeprecate.cs b/Rdmp.Core/CommandExecution/AtomicCommands/ExecuteCommandDeprecate.cs
index 86851ecc09..acdd6f89f0 100644
--- a/Rdmp.Core/CommandExecution/AtomicCommands/ExecuteCommandDeprecate.cs
+++ b/Rdmp.Core/CommandExecution/AtomicCommands/ExecuteCommandDeprecate.cs
@@ -7,6 +7,7 @@
 using Rdmp.Core.Curation.Data;
 using Rdmp.Core.MapsDirectlyToDatabaseTable;
 using Rdmp.Core.Repositories.Construction;
+using System.Linq;
 
 namespace Rdmp.Core.CommandExecution.AtomicCommands;
 
@@ -14,6 +15,8 @@ public class ExecuteCommandDeprecate : BasicCommandExecution
 {
     private readonly IMightBeDeprecated[] _o;
     private readonly bool _desiredState;
+    private readonly IBasicActivateItems _activeItems;
+
 
     [UseWithObjectConstructor]
     public ExecuteCommandDeprecate(IBasicActivateItems itemActivator,
@@ -24,6 +27,7 @@ public ExecuteCommandDeprecate(IBasicActivateItems itemActivator,
     {
         _o = o;
         _desiredState = desiredState;
+        _activeItems = itemActivator;
     }
 
     public override string GetCommandName() => !string.IsNullOrEmpty(OverrideCommandName) ? OverrideCommandName :
@@ -45,8 +49,17 @@ private void ExecuteImpl()
         {
             o.IsDeprecated = _desiredState;
             o.SaveToDatabase();
+            if (!_desiredState && o.GetType() == typeof(Catalogue))//false is not-depricated
+            {
+                var c = (Catalogue) o;
+                var replacedBy = _activeItems.RepositoryLocator.CatalogueRepository.GetExtendedProperties(ExtendedProperty.ReplacedBy);
+                var replacement = replacedBy.Where(rb => rb.ReferencedObjectID == c.ID).FirstOrDefault();
+                replacement.DeleteInDatabase();
+            }
         }
 
+       
+
         if (!BasicActivator.IsInteractive || _o.Length != 1 || _o[0] is not Catalogue || !_desiredState ||
             !BasicActivator.YesNo("Do you have a replacement Catalogue you want to link?", "Replacement")) return;
         var cmd = new ExecuteCommandReplacedBy(BasicActivator, _o[0], null)