diff --git a/assignment-client/src/Agent.cpp b/assignment-client/src/Agent.cpp
index 65e193dec6..327f6de695 100644
--- a/assignment-client/src/Agent.cpp
+++ b/assignment-client/src/Agent.cpp
@@ -476,7 +476,7 @@ void Agent::aboutToFinish() {
     setIsAvatar(false);// will stop timers for sending identity packets
 
     if (_scriptEngine) {
-        _scriptEngine->stop();
+        _scriptEngine->stop(false);
     }
 
     // our entity tree is going to go away so tell that to the EntityScriptingInterface
diff --git a/libraries/entities-renderer/src/EntityTreeRenderer.cpp b/libraries/entities-renderer/src/EntityTreeRenderer.cpp
index 56f6438e70..bc3c6b2441 100644
--- a/libraries/entities-renderer/src/EntityTreeRenderer.cpp
+++ b/libraries/entities-renderer/src/EntityTreeRenderer.cpp
@@ -114,7 +114,7 @@ void EntityTreeRenderer::clear() {
         // Unload and stop the engine here (instead of in its deleter) to
         // avoid marshalling unload signals back to this thread
         _entitiesScriptEngine->unloadAllEntityScripts();
-        _entitiesScriptEngine->stop();
+        _entitiesScriptEngine->stop(false);
     }
 
     if (_wantScripts && !_shuttingDown) {
diff --git a/libraries/script-engine/src/ScriptEngine.cpp b/libraries/script-engine/src/ScriptEngine.cpp
index e7938ac5a0..61ab8c0c63 100644
--- a/libraries/script-engine/src/ScriptEngine.cpp
+++ b/libraries/script-engine/src/ScriptEngine.cpp
@@ -290,7 +290,7 @@ void ScriptEngine::waitTillDoneRunning() {
         assert(workerThread != QThread::currentThread());
 
         // Engine should be stopped already, but be defensive
-        stop();
+        stop(false);
 
         auto startedWaiting = usecTimestampNow();
         while (workerThread->isRunning()) {
@@ -941,13 +941,15 @@ void ScriptEngine::stopAllTimersForEntityScript(const EntityItemID& entityID) {
 
 }
 
-void ScriptEngine::stop() {
+void ScriptEngine::stop(bool marshal) {
     _isStopping = true; // this can be done on any thread
 
     // marshal us over to the correct thread
-    if (QThread::currentThread() != thread()) {
-        QMetaObject::invokeMethod(this, "stop");
-        return;
+    if (marshal) {
+        if (QThread::currentThread() != thread()) {
+            QMetaObject::invokeMethod(this, "stop");
+            return;
+        }
     }
     if (!_isFinished) {
         _isFinished = true;
diff --git a/libraries/script-engine/src/ScriptEngine.h b/libraries/script-engine/src/ScriptEngine.h
index ef7e075021..4d39365626 100644
--- a/libraries/script-engine/src/ScriptEngine.h
+++ b/libraries/script-engine/src/ScriptEngine.h
@@ -84,7 +84,7 @@ public:
 
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
     // NOTE - this is intended to be a public interface for Agent scripts, and local scripts, but not for EntityScripts
-    Q_INVOKABLE void stop(); // this can be called from any thread
+    Q_INVOKABLE void stop(bool marshal); // this can be called from any thread
 
     // Stop any evaluating scripts and wait for the scripting thread to finish.
     void waitTillDoneRunning();
diff --git a/libraries/script-engine/src/ScriptEngines.cpp b/libraries/script-engine/src/ScriptEngines.cpp
index 5e5b8bfde9..6575a12c99 100644
--- a/libraries/script-engine/src/ScriptEngines.cpp
+++ b/libraries/script-engine/src/ScriptEngines.cpp
@@ -160,7 +160,7 @@ void ScriptEngines::shutdownScripting() {
             scriptEngine->disconnect(this);
 
             // Gracefully stop the engine's scripting thread
-            scriptEngine->stop();
+            scriptEngine->stop(false);
 
             // We need to wait for the engine to be done running before we proceed, because we don't
             // want any of the scripts final "scriptEnding()" or pending "update()" methods from accessing
@@ -359,7 +359,10 @@ QStringList ScriptEngines::getRunningScripts() {
     QList<QUrl> urls = _scriptEnginesHash.keys();
     QStringList result;
     for (auto url : urls) {
-        result.append(url.toString());
+        ScriptEngine* engine = getScriptEngineInternal(url);
+        if (engine) {
+            result.append(url.toString());
+        }
     }
     return result;
 }
@@ -388,7 +391,7 @@ void ScriptEngines::stopAllScripts(bool restart) {
                 reloadScript(scriptName);
             });
         }
-        it.value()->stop();
+        it.value()->stop(true);
         qCDebug(scriptengine) << "stopping script..." << it.key();
     }
 }
@@ -411,7 +414,7 @@ bool ScriptEngines::stopScript(const QString& rawScriptURL, bool restart) {
                     reloadScript(scriptName);
                 });
             }
-            scriptEngine->stop();
+            scriptEngine->stop(false);
             stoppedScript = true;
             qCDebug(scriptengine) << "stopping script..." << scriptURL;
         }
@@ -459,7 +462,7 @@ ScriptEngine* ScriptEngines::loadScript(const QUrl& scriptFilename, bool isUserL
     }
 
     auto scriptEngine = getScriptEngine(scriptUrl);
-    if (scriptEngine) {
+    if (scriptEngine && !scriptEngine->isStopping()) {
         return scriptEngine;
     }
 
@@ -484,19 +487,21 @@ ScriptEngine* ScriptEngines::loadScript(const QUrl& scriptFilename, bool isUserL
     return scriptEngine;
 }
 
-ScriptEngine* ScriptEngines::getScriptEngine(const QUrl& rawScriptURL) {
+ScriptEngine* ScriptEngines::getScriptEngineInternal(const QUrl& rawScriptURL) {
     ScriptEngine* result = nullptr;
-    {
-        QReadLocker lock(&_scriptEnginesHashLock);
-        const QUrl scriptURL = normalizeScriptURL(rawScriptURL);
-        auto it = _scriptEnginesHash.find(scriptURL);
-        if (it != _scriptEnginesHash.end() && !it.value()->isStopping()) {
-            result = it.value();
-        }
+    const QUrl scriptURL = normalizeScriptURL(rawScriptURL);
+    auto it = _scriptEnginesHash.find(scriptURL);
+    if (it != _scriptEnginesHash.end()) {
+        result = it.value();
     }
     return result;
 }
 
+ScriptEngine* ScriptEngines::getScriptEngine(const QUrl& rawScriptURL) {
+    QReadLocker lock(&_scriptEnginesHashLock);
+    return getScriptEngineInternal(rawScriptURL);
+}
+
 // FIXME - change to new version of ScriptCache loading notification
 void ScriptEngines::onScriptEngineLoaded(const QString& rawScriptURL) {
     UserActivityLogger::getInstance().loadedScript(rawScriptURL);
diff --git a/libraries/script-engine/src/ScriptEngines.h b/libraries/script-engine/src/ScriptEngines.h
index a9c273b2a7..6d887ce95f 100644
--- a/libraries/script-engine/src/ScriptEngines.h
+++ b/libraries/script-engine/src/ScriptEngines.h
@@ -87,6 +87,7 @@ protected:
     void onScriptEngineLoaded(const QString& scriptFilename);
     void onScriptEngineError(const QString& scriptFilename);
     void launchScriptEngine(ScriptEngine* engine);
+    ScriptEngine* getScriptEngineInternal(const QUrl& rawScriptURL);
 
     QReadWriteLock _scriptEnginesHashLock;
     QHash<QUrl, ScriptEngine*> _scriptEnginesHash;