Index: Riskeer/Integration/test/Riskeer.Integration.Service.Test/RiskeerDataSynchronizationServiceTest.cs
===================================================================
diff -u -rb14f85d007791f99296896e4a940a0e97ae6d8cf -r270ab241e81b1049a6dc9ef0ce540f290039e82e
--- Riskeer/Integration/test/Riskeer.Integration.Service.Test/RiskeerDataSynchronizationServiceTest.cs	(.../RiskeerDataSynchronizationServiceTest.cs)	(revision b14f85d007791f99296896e4a940a0e97ae6d8cf)
+++ Riskeer/Integration/test/Riskeer.Integration.Service.Test/RiskeerDataSynchronizationServiceTest.cs	(.../RiskeerDataSynchronizationServiceTest.cs)	(revision 270ab241e81b1049a6dc9ef0ce540f290039e82e)
@@ -277,7 +277,10 @@
                                                             .Select(c => c.InputParameters)
                                                             .Where(i => i.HydraulicBoundaryLocation != null));
             expectedAffectedItems.AddRange(assessmentSection.Piping.Calculations
-                                                            .Cast<IPipingCalculationScenario<PipingInput>>()
+                                                            .OfType<SemiProbabilisticPipingCalculationScenario>()
+                                                            .Where(c => !c.InputParameters.UseAssessmentLevelManualInput && c.HasOutput));
+            expectedAffectedItems.AddRange(assessmentSection.Piping.Calculations
+                                                            .OfType<ProbabilisticPipingCalculationScenario>()
                                                             .Where(c => c.HasOutput));
             expectedAffectedItems.AddRange(assessmentSection.Piping.Calculations
                                                             .Cast<IPipingCalculationScenario<PipingInput>>()
@@ -326,8 +329,12 @@
                                            .All(c => c.InputParameters.HydraulicBoundaryLocation == null && !c.HasOutput));
             Assert.IsTrue(assessmentSection.HeightStructures.Calculations.Cast<StructuresCalculation<HeightStructuresInput>>()
                                            .All(c => c.InputParameters.HydraulicBoundaryLocation == null && !c.HasOutput));
+            Assert.IsTrue(assessmentSection.Piping.Calculations.OfType<SemiProbabilisticPipingCalculationScenario>()
+                                           .All(c => !c.InputParameters.UseAssessmentLevelManualInput && !c.HasOutput));
+            Assert.IsTrue(assessmentSection.Piping.Calculations.OfType<ProbabilisticPipingCalculationScenario>()
+                                           .All(c => !c.HasOutput));
             Assert.IsTrue(assessmentSection.Piping.Calculations.Cast<IPipingCalculationScenario<PipingInput>>()
-                                           .All(c => c.InputParameters.HydraulicBoundaryLocation == null && !c.HasOutput));
+                                           .All(c => c.InputParameters.HydraulicBoundaryLocation == null));
             Assert.IsTrue(assessmentSection.StabilityPointStructures.Calculations.Cast<StructuresCalculation<StabilityPointStructuresInput>>()
                                            .All(c => c.InputParameters.HydraulicBoundaryLocation == null && !c.HasOutput));
             Assert.IsTrue(assessmentSection.StabilityStoneCover.Calculations.Cast<StabilityStoneCoverWaveConditionsCalculation>()
Index: Riskeer/Piping/src/Riskeer.Piping.Service/PipingDataSynchronizationService.cs
===================================================================
diff -u -rde851b1488ab6396c74afda4993973752252f0cc -r270ab241e81b1049a6dc9ef0ce540f290039e82e
--- Riskeer/Piping/src/Riskeer.Piping.Service/PipingDataSynchronizationService.cs	(.../PipingDataSynchronizationService.cs)	(revision de851b1488ab6396c74afda4993973752252f0cc)
+++ Riskeer/Piping/src/Riskeer.Piping.Service/PipingDataSynchronizationService.cs	(.../PipingDataSynchronizationService.cs)	(revision 270ab241e81b1049a6dc9ef0ce540f290039e82e)
@@ -128,7 +128,13 @@
         }
 
         /// <summary>
-        /// Clears the <see cref="HydraulicBoundaryLocation"/> and output for all the calculations in the <see cref="PipingFailureMechanism"/>.
+        /// Clears:
+        /// <list type="bullet">
+        /// <item>The <see cref="HydraulicBoundaryLocation"/> for all the calculations in the <see cref="PipingFailureMechanism"/>;</item>
+        /// <item>The output for all the calculations in the <see cref="PipingFailureMechanism"/>,
+        /// except for the <see cref="SemiProbabilisticPipingCalculationScenario"/> where
+        /// <see cref="SemiProbabilisticPipingInput.UseAssessmentLevelManualInput"/> is <c>true</c>.</item>
+        /// </list>
         /// </summary>
         /// <param name="failureMechanism">The <see cref="PipingFailureMechanism"/> which contains the calculations.</param>
         /// <returns>An <see cref="IEnumerable{T}"/> of objects which are affected by removing data.</returns>
@@ -141,13 +147,15 @@
             }
 
             var affectedItems = new List<IObservable>();
+            affectedItems.AddRange(ClearAllSemiProbabilisticCalculationOutputWithoutManualAssessmentLevel(failureMechanism));
+            affectedItems.AddRange(ClearAllProbabilisticCalculationOutput(failureMechanism));
+
             foreach (IPipingCalculationScenario<PipingInput> calculation in failureMechanism.Calculations.Cast<IPipingCalculationScenario<PipingInput>>())
             {
-                affectedItems.AddRange(ClearCalculationOutput(calculation)
-                                           .Concat(ClearHydraulicBoundaryLocation(calculation.InputParameters)));
+                affectedItems.AddRange(ClearHydraulicBoundaryLocation(calculation.InputParameters));
             }
 
-            return affectedItems;
+            return affectedItems.Distinct();
         }
 
         /// <summary>
Index: Riskeer/Piping/test/Riskeer.Piping.Service.Test/PipingDataSynchronizationServiceTest.cs
===================================================================
diff -u -r2c97f863718888be8f3b35f4934c0119869b9187 -r270ab241e81b1049a6dc9ef0ce540f290039e82e
--- Riskeer/Piping/test/Riskeer.Piping.Service.Test/PipingDataSynchronizationServiceTest.cs	(.../PipingDataSynchronizationServiceTest.cs)	(revision 2c97f863718888be8f3b35f4934c0119869b9187)
+++ Riskeer/Piping/test/Riskeer.Piping.Service.Test/PipingDataSynchronizationServiceTest.cs	(.../PipingDataSynchronizationServiceTest.cs)	(revision 270ab241e81b1049a6dc9ef0ce540f290039e82e)
@@ -238,28 +238,32 @@
         {
             // Setup
             PipingFailureMechanism failureMechanism = PipingTestDataGenerator.GetPipingFailureMechanismWithAllCalculationConfigurations();
-            IPipingCalculationScenario<PipingInput>[] calculations = failureMechanism.Calculations.Cast<IPipingCalculationScenario<PipingInput>>().ToArray();
-            IObservable[] expectedAffectedCalculations = calculations.Where(c => c.HasOutput)
-                                                                     .Cast<IObservable>()
-                                                                     .ToArray();
-            IObservable[] expectedAffectedCalculationInputs = calculations.Select(c => c.InputParameters)
-                                                                          .Where(i => i.HydraulicBoundaryLocation != null)
-                                                                          .Cast<IObservable>()
-                                                                          .ToArray();
+            IPipingCalculationScenario<PipingInput>[] calculations = failureMechanism.Calculations.Cast<IPipingCalculationScenario<PipingInput>>()
+                                                                                     .ToArray();
+            
+            var expectedAffectedItems = new List<IObservable>();
+            expectedAffectedItems.AddRange(calculations.OfType<SemiProbabilisticPipingCalculationScenario>()
+                                                       .Where(c => !c.InputParameters.UseAssessmentLevelManualInput
+                                                                   && c.HasOutput));
+            expectedAffectedItems.AddRange(calculations.OfType<ProbabilisticPipingCalculationScenario>()
+                                                       .Where(c => c.HasOutput));
+            expectedAffectedItems.AddRange(calculations.Select(c => c.InputParameters)
+                                                       .Where(i => i.HydraulicBoundaryLocation != null));
 
             // Call
             IEnumerable<IObservable> affectedItems = PipingDataSynchronizationService.ClearAllCalculationOutputAndHydraulicBoundaryLocations(failureMechanism);
 
             // Assert
             // Note: To make sure the clear is performed regardless of what is done with
             // the return result, no ToArray() should be called before these assertions:
-            Assert.IsTrue(failureMechanism.Calculations
-                                          .Cast<IPipingCalculationScenario<PipingInput>>()
-                                          .All(c => c.InputParameters.HydraulicBoundaryLocation == null
-                                                    && !c.HasOutput));
+            Assert.IsTrue(calculations.OfType<SemiProbabilisticPipingCalculationScenario>()
+                                      .Where(c => !c.InputParameters.UseAssessmentLevelManualInput)
+                                      .All(c => !c.HasOutput));
+            Assert.IsTrue(calculations.OfType<ProbabilisticPipingCalculationScenario>()
+                                      .All(c => !c.HasOutput));
+            Assert.IsTrue(calculations.All(c => c.InputParameters.HydraulicBoundaryLocation == null));
 
-            CollectionAssert.AreEquivalent(expectedAffectedCalculations.Concat(expectedAffectedCalculationInputs),
-                                           affectedItems);
+            CollectionAssert.AreEquivalent(expectedAffectedItems, affectedItems);
         }
 
         [Test]