Index: Ringtoets/HeightStructures/src/Ringtoets.HeightStructures.Plugin/HeightStructuresPlugin.cs
===================================================================
diff -u -rd93d1c16b0543964ba4202f9faa7a74a6cd4a467 -r9b0d18547885c18342a9ab149538b137f0b004d0
--- Ringtoets/HeightStructures/src/Ringtoets.HeightStructures.Plugin/HeightStructuresPlugin.cs	(.../HeightStructuresPlugin.cs)	(revision d93d1c16b0543964ba4202f9faa7a74a6cd4a467)
+++ Ringtoets/HeightStructures/src/Ringtoets.HeightStructures.Plugin/HeightStructuresPlugin.cs	(.../HeightStructuresPlugin.cs)	(revision 9b0d18547885c18342a9ab149538b137f0b004d0)
@@ -101,10 +101,7 @@
                 FileFilterGenerator = CreateHeightStructureFileFilter(),
                 CreateFileImporter = (context, filePath) => CreateHeightStructuresImporter(
                     context, filePath, new ImportMessageProvider(), new HeightStructureReplaceDataStrategy(context.FailureMechanism)),
-                VerifyUpdates = context =>
-                    VerifyStructuresShouldUpdate(
-                        context.FailureMechanism,
-                        RingtoetsCommonIOResources.VerifyStructuresShouldUpdate_When_importing_Calculation_with_Structure_data_output_will_be_cleared_confirm)
+                VerifyUpdates = VerifyStructuresShouldUpdateOnImport
             };
 
             yield return RingtoetsImportInfoFactory.CreateCalculationConfigurationImportInfo<HeightStructuresCalculationGroupContext>(
@@ -129,10 +126,7 @@
                 CreateFileImporter = (context, filePath) => CreateHeightStructuresImporter(
                     context, filePath, new UpdateMessageProvider(), new HeightStructureUpdateDataStrategy(context.FailureMechanism)),
                 CurrentPath = context => context.WrappedData.SourcePath,
-                VerifyUpdates = context =>
-                    VerifyStructuresShouldUpdate(
-                        context.FailureMechanism,
-                        RingtoetsCommonIOResources.VerifyStructuresShouldUpdate_When_updating_Calculation_with_Structure_data_output_will_be_cleared_confirm)
+                VerifyUpdates = VerifyStructuresShouldUpdateOnUpdate
             };
         }
 
@@ -885,6 +879,55 @@
                                            RingtoetsCommonIOResources.Shape_file_filter_Description);
         }
 
+        private bool VerifyStructuresShouldUpdateOnImport(HeightStructuresContext context)
+        {
+            IFailureMechanism failureMechanism = context.FailureMechanism;
+
+            bool hasStructureAndOutput = failureMechanism.Calculations
+                                                         .Cast<StructuresCalculation<HeightStructuresInput>>()
+                                                         .Any(c => c.InputParameters.Structure != null
+                                                                   && c.HasOutput);
+
+            return !hasStructureAndOutput
+                   || VerifyStructuresShouldUpdate(
+                       failureMechanism,
+                       RingtoetsCommonIOResources.VerifyStructuresShouldUpdate_When_importing_Calculation_with_Structure_data_output_will_be_cleared_confirm);
+        }
+
+        /// <summary>
+        /// Class for comparing <see cref="StructureBase"/> by only the id.
+        /// </summary>
+        private class StructureIdEqualityComparer : IEqualityComparer<StructureBase>
+        {
+            public bool Equals(StructureBase x, StructureBase y)
+            {
+                return x.Id.Equals(y.Id);
+            }
+
+            public int GetHashCode(StructureBase obj)
+            {
+                return obj.Id.GetHashCode();
+            }
+        }
+
+        private bool VerifyStructuresShouldUpdateOnUpdate(HeightStructuresContext context)
+        {
+            StructureCollection<HeightStructure> heightStructures = context.WrappedData;
+            IFailureMechanism failureMechanism = context.FailureMechanism;
+            var comparer = new StructureIdEqualityComparer();
+
+            bool hasRemovedStructure = context.FailureMechanism.Calculations
+                                              .Cast<StructuresCalculation<HeightStructuresInput>>()
+                                              .Any(c => c.InputParameters.Structure != null
+                                                        && c.HasOutput
+                                                        && !heightStructures.Contains(c.InputParameters.Structure, comparer));
+
+            return !hasRemovedStructure
+                   || VerifyStructuresShouldUpdate(
+                       failureMechanism,
+                       RingtoetsCommonIOResources.VerifyStructuresShouldUpdate_When_updating_Calculation_with_Structure_data_output_will_be_cleared_confirm);
+        }
+
         private bool VerifyStructuresShouldUpdate(IFailureMechanism failureMechanism, string query)
         {
             var changeHandler = new FailureMechanismCalculationChangeHandler(failureMechanism,