Index: Riskeer/Integration/src/Riskeer.Integration.Service/Comparers/AssessmentSectionMergeComparer.cs
===================================================================
diff -u -rfdc2f4a655bcb8d2b7e3319067c5f9bcc5543e21 -r2d6e384d5520384b2c8b7dea57673bd6025bb615
--- Riskeer/Integration/src/Riskeer.Integration.Service/Comparers/AssessmentSectionMergeComparer.cs	(.../AssessmentSectionMergeComparer.cs)	(revision fdc2f4a655bcb8d2b7e3319067c5f9bcc5543e21)
+++ Riskeer/Integration/src/Riskeer.Integration.Service/Comparers/AssessmentSectionMergeComparer.cs	(.../AssessmentSectionMergeComparer.cs)	(revision 2d6e384d5520384b2c8b7dea57673bd6025bb615)
@@ -80,9 +80,21 @@
         private static bool AreHydraulicBoundaryDataInstancesEquivalent(HydraulicBoundaryData hydraulicBoundaryData,
                                                                         HydraulicBoundaryData otherHydraulicBoundaryData)
         {
-            return hydraulicBoundaryData.Version == otherHydraulicBoundaryData.Version
-                   && AreHydraulicLocationConfigurationDatabasesEquivalent(hydraulicBoundaryData.HydraulicLocationConfigurationDatabase,
-                                                                           otherHydraulicBoundaryData.HydraulicLocationConfigurationDatabase);
+            if (AreHydraulicLocationConfigurationDatabasesEquivalent(
+                    hydraulicBoundaryData.HydraulicLocationConfigurationDatabase, otherHydraulicBoundaryData.HydraulicLocationConfigurationDatabase))
+            {
+                for (var i = 0; i < hydraulicBoundaryData.HydraulicBoundaryDatabases.Count; i++)
+                {
+                    if (!AreHydraulicBoundaryDatabasesEquivalent(hydraulicBoundaryData.HydraulicBoundaryDatabases[i], otherHydraulicBoundaryData.HydraulicBoundaryDatabases[i]))
+                    {
+                        return false;
+                    }
+                }
+
+                return true;
+            }
+
+            return false;
         }
 
         private static bool AreHydraulicLocationConfigurationDatabasesEquivalent(HydraulicLocationConfigurationDatabase hydraulicLocationConfigurationDatabase,
@@ -100,6 +112,13 @@
                    && hydraulicLocationConfigurationDatabase.Comment == otherHydraulicLocationConfigurationDatabase.Comment;
         }
 
+        private static bool AreHydraulicBoundaryDatabasesEquivalent(HydraulicBoundaryDatabase hydraulicBoundaryDatabase,
+                                                                    HydraulicBoundaryDatabase otherHydraulicBoundaryDatabase)
+        {
+            return hydraulicBoundaryDatabase.Version == otherHydraulicBoundaryDatabase.Version
+                   && hydraulicBoundaryDatabase.UsePreprocessorClosure == otherHydraulicBoundaryDatabase.UsePreprocessorClosure;
+        }
+
         private static bool AreFailureMechanismContributionsEquivalent(FailureMechanismContribution failureMechanismContribution,
                                                                        FailureMechanismContribution otherFailureMechanismContribution)
         {
Index: Riskeer/Integration/test/Riskeer.Integration.Service.Test/Comparers/AssessmentSectionMergeComparerTest.cs
===================================================================
diff -u -rfdc2f4a655bcb8d2b7e3319067c5f9bcc5543e21 -r2d6e384d5520384b2c8b7dea57673bd6025bb615
--- Riskeer/Integration/test/Riskeer.Integration.Service.Test/Comparers/AssessmentSectionMergeComparerTest.cs	(.../AssessmentSectionMergeComparerTest.cs)	(revision fdc2f4a655bcb8d2b7e3319067c5f9bcc5543e21)
+++ Riskeer/Integration/test/Riskeer.Integration.Service.Test/Comparers/AssessmentSectionMergeComparerTest.cs	(.../AssessmentSectionMergeComparerTest.cs)	(revision 2d6e384d5520384b2c8b7dea57673bd6025bb615)
@@ -150,6 +150,32 @@
             Assert.IsFalse(result);
         }
 
+        [Test]
+        [TestCaseSource(nameof(GetAssessmentSectionWithNotEquivalentHydraulicBoundaryDatabaseTestCases))]
+        public void Compare_AssessmentSectionWithNotEquivalentHydraulicBoundaryDatabase_ReturnsFalse(AssessmentSection otherAssessmentSection)
+        {
+            // Setup
+            AssessmentSection assessmentSection = CreateAssessmentSection();
+            assessmentSection.HydraulicBoundaryData.HydraulicBoundaryDatabases.Add(CreateHydraulicBoundaryDatabase());
+
+            var comparer = new AssessmentSectionMergeComparer();
+
+            // Call
+            bool result = comparer.Compare(assessmentSection, otherAssessmentSection);
+
+            // Assert
+            Assert.IsFalse(result);
+        }
+
+        private static HydraulicBoundaryDatabase CreateHydraulicBoundaryDatabase()
+        {
+            return new HydraulicBoundaryDatabase
+            {
+                Version = "Version",
+                UsePreprocessorClosure = false
+            };
+        }
+
         private static AssessmentSection CreateAssessmentSection()
         {
             var assessmentSection = new AssessmentSection(AssessmentSectionComposition.Dike, 0.1, 0.025);
@@ -206,9 +232,6 @@
                 sec => sec.Id = "DifferentVersion",
                 "Id");
             yield return new ChangePropertyData<AssessmentSection>(
-                sec => sec.HydraulicBoundaryData.Version = "DifferentVersion",
-                "HydraulicBoundaryData");
-            yield return new ChangePropertyData<AssessmentSection>(
                 sec => sec.FailureMechanismContribution.MaximumAllowableFloodingProbability -= 1e-15,
                 "MaximumAllowableFloodingProbability");
             yield return new ChangePropertyData<AssessmentSection>(
@@ -317,5 +340,27 @@
                 },
                 "Different Comment");
         }
+
+        private static IEnumerable<TestCaseData> GetAssessmentSectionWithNotEquivalentHydraulicBoundaryDatabaseTestCases()
+        {
+            foreach (ChangePropertyData<HydraulicBoundaryDatabase> changeSingleDataProperty in ChangeSingleDataOfHydraulicBoundaryDatabase())
+            {
+                HydraulicBoundaryDatabase hydraulicBoundaryDatabase = CreateHydraulicBoundaryDatabase();
+                AssessmentSection assessmentSection = CreateAssessmentSection();
+                assessmentSection.HydraulicBoundaryData.HydraulicBoundaryDatabases.Add(hydraulicBoundaryDatabase);
+                changeSingleDataProperty.ActionToChangeProperty(hydraulicBoundaryDatabase);
+                yield return new TestCaseData(assessmentSection).SetName(changeSingleDataProperty.PropertyName);
+            }
+        }
+
+        private static IEnumerable<ChangePropertyData<HydraulicBoundaryDatabase>> ChangeSingleDataOfHydraulicBoundaryDatabase()
+        {
+            yield return new ChangePropertyData<HydraulicBoundaryDatabase>(
+                hydraulicBoundaryDatabase => hydraulicBoundaryDatabase.Version = "Other Version",
+                "Different Version");
+            yield return new ChangePropertyData<HydraulicBoundaryDatabase>(
+                hydraulicBoundaryDatabase => hydraulicBoundaryDatabase.UsePreprocessorClosure = !hydraulicBoundaryDatabase.UsePreprocessorClosure,
+                "Different UsePreprocessorClosure");
+        }
     }
 }
\ No newline at end of file