diff --git a/src/plugins/cmakeprojectmanager/cmakebuildconfiguration.cpp b/src/plugins/cmakeprojectmanager/cmakebuildconfiguration.cpp
index d7ecacc0668..4a39dd9d3b8 100644
--- a/src/plugins/cmakeprojectmanager/cmakebuildconfiguration.cpp
+++ b/src/plugins/cmakeprojectmanager/cmakebuildconfiguration.cpp
@@ -365,7 +365,6 @@ CMakeBuildSettingsWidget::CMakeBuildSettingsWidget(CMakeBuildConfiguration *bc)
     }
 
     connect(bc->buildSystem(), &BuildSystem::parsingFinished, this, [this, stretcher] {
-        m_configModel->flush();
         m_configModel->setConfiguration(m_buildConfiguration->configurationFromCMake());
         m_configModel->setInitialParametersConfiguration(
             m_buildConfiguration->initialCMakeConfiguration());
@@ -1622,6 +1621,8 @@ void InitialCMakeArgumentsAspect::setAllValues(const QString &values, QStringLis
             arg.replace("-T", "-DCMAKE_GENERATOR_TOOLSET:STRING=");
     }
     m_cmakeConfiguration = CMakeConfig::fromArguments(arguments, additionalArguments);
+    for (CMakeConfigItem &ci : m_cmakeConfiguration)
+        ci.isInitial = true;
 
     // Display the unknown arguments in "Additional CMake parameters"
     const QString additionalArgumentsValue = ProcessArgs::joinArgs(additionalArguments);
@@ -1631,6 +1632,8 @@ void InitialCMakeArgumentsAspect::setAllValues(const QString &values, QStringLis
 void InitialCMakeArgumentsAspect::setCMakeConfiguration(const CMakeConfig &config)
 {
     m_cmakeConfiguration = config;
+    for (CMakeConfigItem &ci : m_cmakeConfiguration)
+        ci.isInitial = true;
 }
 
 void InitialCMakeArgumentsAspect::fromMap(const QVariantMap &map)
diff --git a/src/plugins/cmakeprojectmanager/configmodel.cpp b/src/plugins/cmakeprojectmanager/configmodel.cpp
index aa74f3986b6..fe11f9367b5 100644
--- a/src/plugins/cmakeprojectmanager/configmodel.cpp
+++ b/src/plugins/cmakeprojectmanager/configmodel.cpp
@@ -272,46 +272,61 @@ void ConfigModel::setInitialParametersConfiguration(const CMakeConfig &config)
 
 void ConfigModel::setConfiguration(const QList<ConfigModel::InternalDataItem> &config)
 {
-    QList<InternalDataItem> tmp = config;
-    auto newIt = tmp.constBegin();
-    auto newEndIt = tmp.constEnd();
-    auto oldIt = m_configuration.constBegin();
-    auto oldEndIt = m_configuration.constEnd();
+    auto mergeLists = [](const QList<InternalDataItem> &oldList,
+                         const QList<InternalDataItem> &newList) -> QList<InternalDataItem> {
+        auto newIt = newList.constBegin();
+        auto newEndIt = newList.constEnd();
+        auto oldIt = oldList.constBegin();
+        auto oldEndIt = oldList.constEnd();
 
-    QList<InternalDataItem> result;
-    while (newIt != newEndIt && oldIt != oldEndIt) {
-        if (oldIt->isUnset) {
-            ++oldIt;
-        } else if (newIt->isHidden || newIt->isUnset) {
-            ++newIt;
-        } else if (newIt->key < oldIt->key) {
-            // Add new entry:
-            result << *newIt;
-            ++newIt;
-        } else if (newIt->key > oldIt->key) {
-            // Keep old user settings, but skip other entries:
-            if (oldIt->isUserChanged || oldIt->isUserNew)
-                result << InternalDataItem(*oldIt);
-            ++oldIt;
-        } else {
-            // merge old/new entry:
-            InternalDataItem item(*newIt);
-            item.newValue = (newIt->value != oldIt->newValue) ? oldIt->newValue : QString();
-            item.isUserChanged = !item.newValue.isEmpty() && (item.newValue != item.value);
-            result << item;
-            ++newIt;
-            ++oldIt;
+        QList<InternalDataItem> result;
+        while (newIt != newEndIt && oldIt != oldEndIt) {
+            if (oldIt->isUnset) {
+                ++oldIt;
+            } else if (newIt->isHidden || newIt->isUnset) {
+                ++newIt;
+            } else if (newIt->key < oldIt->key) {
+                // Add new entry:
+                result << *newIt;
+                ++newIt;
+            } else if (newIt->key > oldIt->key) {
+                // Keep old user settings, but skip other entries:
+                if (oldIt->isUserChanged || oldIt->isUserNew)
+                    result << InternalDataItem(*oldIt);
+                ++oldIt;
+            } else {
+                // merge old/new entry:
+                InternalDataItem item(*newIt);
+                item.newValue = (newIt->value != oldIt->newValue) ? oldIt->newValue : QString();
+                item.isUserChanged = !item.newValue.isEmpty() && (item.newValue != item.value);
+                result << item;
+                ++newIt;
+                ++oldIt;
+            }
         }
-    }
 
-    // Add remaining new entries:
-    for (; newIt != newEndIt; ++newIt) {
-        if (newIt->isHidden)
-            continue;
-        result << InternalDataItem(*newIt);
-    }
+        // Add remaining new entries:
+        for (; newIt != newEndIt; ++newIt) {
+            if (newIt->isHidden)
+                continue;
+            result << InternalDataItem(*newIt);
+        }
 
-    m_configuration = result;
+        return result;
+    };
+
+    auto isInitial = [](const InternalDataItem &i) { return i.isInitial; };
+
+    QList<InternalDataItem> initialOld;
+    QList<InternalDataItem> currentOld;
+    std::tie(initialOld, currentOld) = Utils::partition(m_configuration, isInitial);
+
+    QList<InternalDataItem> initialNew;
+    QList<InternalDataItem> currentNew;
+    std::tie(initialNew, currentNew) = Utils::partition(config, isInitial);
+
+    m_configuration = mergeLists(initialOld, initialNew);
+    m_configuration.append(mergeLists(currentOld, currentNew));
 
     generateTree();
 }