diff --git a/src/Config.cpp b/src/Config.cpp
index c035e84d..78117cf6 100644
--- a/src/Config.cpp
+++ b/src/Config.cpp
@@ -84,7 +84,7 @@ Config::Flags Config::flags() const
 void Config::setFlags(Flags f)
 {
     auto dr = DockRegistry::self();
-    if (!dr->isEmpty()) {
+    if (!dr->isEmpty(/*excludeBeingDeleted=*/ true)) {
         qWarning() << Q_FUNC_INFO << "Only use this function at startup before creating any DockWidget or MainWindow"
                    << "; These are already created: " << dr->mainWindowsNames()
                    << dr->dockWidgetNames() << dr->floatingWindows();
@@ -138,7 +138,7 @@ int Config::separatorThickness() const
 
 void Config::setSeparatorThickness(int value)
 {
-    if (!DockRegistry::self()->isEmpty()) {
+    if (!DockRegistry::self()->isEmpty(/*excludeBeingDeleted=*/ true)) {
         qWarning() << Q_FUNC_INFO << "Only use this function at startup before creating any DockWidget or MainWindow";
         return;
     }
diff --git a/src/private/DockRegistry.cpp b/src/private/DockRegistry.cpp
index 802dcf9e..95a38569 100644
--- a/src/private/DockRegistry.cpp
+++ b/src/private/DockRegistry.cpp
@@ -100,9 +100,13 @@ void DockRegistry::onFocusObjectChanged(QObject *obj)
         Q_EMIT m_focusedDockWidget->isFocusedChanged(true);
 }
 
-bool DockRegistry::isEmpty() const
+bool DockRegistry::isEmpty(bool excludeBeingDeleted) const
 {
-    return m_dockWidgets.isEmpty() && m_mainWindows.isEmpty() && m_floatingWindows.isEmpty();
+    if (!m_dockWidgets.isEmpty() || !m_mainWindows.isEmpty())
+        return false;
+
+    return excludeBeingDeleted ? !hasFloatingWindows()
+                               : m_floatingWindows.isEmpty();
 }
 
 void DockRegistry::checkSanityAll(bool dumpLayout)
@@ -474,6 +478,13 @@ const QVector<QWindow *> DockRegistry::floatingQWindows() const
     return windows;
 }
 
+bool DockRegistry::hasFloatingWindows() const
+{
+    return std::any_of(m_floatingWindows.begin(), m_floatingWindows.end(), [] (FloatingWindow *fw) {
+        return !fw->beingDeleted();
+    });
+}
+
 FloatingWindow *DockRegistry::floatingWindowForHandle(QWindow *windowHandle) const
 {
     for (FloatingWindow *fw : m_floatingWindows) {
diff --git a/src/private/DockRegistry_p.h b/src/private/DockRegistry_p.h
index 7da4e17c..89d69bf5 100644
--- a/src/private/DockRegistry_p.h
+++ b/src/private/DockRegistry_p.h
@@ -89,6 +89,9 @@ public:
     ///@brief overload that returns list of QWindow. This is more friendly for supporting both QtWidgets and QtQuick
     const QVector<QWindow*> floatingQWindows() const;
 
+    ///@brief returns whether if there's at least one floating window
+    bool hasFloatingWindows() const;
+
     ///@brief returns the FloatingWindow with handle @p windowHandle
     FloatingWindow *floatingWindowForHandle(QWindow *windowHandle) const;
 
@@ -127,8 +130,10 @@ public:
 
     /**
      * @brief returns true if there's 0 dockwidgets, 0 main windows
+     *
+     * @param excludeBeingDeleted if true, any window currently being deleted won't count
      */
-    bool isEmpty() const;
+    bool isEmpty(bool excludeBeingDeleted = false) const;
 
     /**
      * @brief Calls MultiSplitter::checkSanity() on all layouts.