diff --git a/src/main/java/org/jabref/gui/ai/components/aichat/AiChatComponent.java b/src/main/java/org/jabref/gui/ai/components/aichat/AiChatComponent.java
index 308b119d3cf..e0ca91845ea 100644
--- a/src/main/java/org/jabref/gui/ai/components/aichat/AiChatComponent.java
+++ b/src/main/java/org/jabref/gui/ai/components/aichat/AiChatComponent.java
@@ -1,6 +1,8 @@
 package org.jabref.gui.ai.components.aichat;
 
 import javafx.application.Platform;
+import javafx.beans.property.IntegerProperty;
+import javafx.beans.property.SimpleIntegerProperty;
 import javafx.fxml.FXML;
 import javafx.scene.control.Button;
 import javafx.scene.control.ProgressIndicator;
@@ -28,6 +30,7 @@
 import dev.langchain4j.data.message.UserMessage;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import scala.concurrent.impl.FutureConvertersImpl;
 
 public class AiChatComponent extends VBox {
     private static final Logger LOGGER = LoggerFactory.getLogger(AiChatComponent.class);
@@ -70,12 +73,6 @@ public void initialize() {
             }
         });
 
-        scrollPane.needsLayoutProperty().addListener((observable, oldValue, newValue) -> {
-            if (!newValue) {
-                scrollPane.setVvalue(1.0);
-            }
-        });
-
         chatVBox
                 .getChildren()
                 .addAll(aiChatLogic.getChatHistory()
diff --git a/src/main/java/org/jabref/logic/ai/FileEmbeddingsManager.java b/src/main/java/org/jabref/logic/ai/FileEmbeddingsManager.java
index 48e07d61a6b..24133bdd1e4 100644
--- a/src/main/java/org/jabref/logic/ai/FileEmbeddingsManager.java
+++ b/src/main/java/org/jabref/logic/ai/FileEmbeddingsManager.java
@@ -54,7 +54,10 @@ public FileEmbeddingsManager(AiPreferences aiPreferences, ReadOnlyBooleanPropert
     }
 
     private void setupListeningToPreferencesChanges() {
-        aiPreferences.addListenerToEmbeddingsParametersChange(embeddingStore::removeAll);
+        aiPreferences.addListenerToEmbeddingsParametersChange(() -> {
+            embeddingStore.removeAll();
+            fullyIngestedDocumentsTracker.unmarkAll();
+        });
     }
 
     public void addDocument(String link, Document document, long modificationTimeInSeconds, IntegerProperty workDone, IntegerProperty workMax) throws InterruptedException {
diff --git a/src/main/java/org/jabref/logic/ai/embeddings/FullyIngestedDocumentsTracker.java b/src/main/java/org/jabref/logic/ai/embeddings/FullyIngestedDocumentsTracker.java
index 90c6e17813c..dbb2fcdc3dc 100644
--- a/src/main/java/org/jabref/logic/ai/embeddings/FullyIngestedDocumentsTracker.java
+++ b/src/main/java/org/jabref/logic/ai/embeddings/FullyIngestedDocumentsTracker.java
@@ -56,4 +56,8 @@ public void unmarkDocumentAsFullyIngested(String link) {
     public Set<String> getFullyIngestedDocuments() {
         return new HashSet<>(ingestedMap.keySet());
     }
+
+    public void unmarkAll() {
+        ingestedMap.clear();
+    }
 }
diff --git a/src/main/java/org/jabref/logic/ai/models/JabRefEmbeddingModel.java b/src/main/java/org/jabref/logic/ai/models/JabRefEmbeddingModel.java
index 7ac288d22a0..451778bcb4e 100644
--- a/src/main/java/org/jabref/logic/ai/models/JabRefEmbeddingModel.java
+++ b/src/main/java/org/jabref/logic/ai/models/JabRefEmbeddingModel.java
@@ -104,13 +104,7 @@ private void setupListeningToPreferencesChanges() {
             }
         });
 
-        aiPreferences.customizeExpertSettingsProperty().addListener((obs, oldValue, newValue) -> {
-            if (newValue && predictorProperty.get().isEmpty()) {
-                startRebuildingTask();
-            }
-        });
-
-        aiPreferences.embeddingModelProperty().addListener(obs -> startRebuildingTask());
+        aiPreferences.addListenerToEmbeddingsParametersChange(this::startRebuildingTask);
     }
 
     @Override
diff --git a/src/main/java/org/jabref/preferences/ai/AiPreferences.java b/src/main/java/org/jabref/preferences/ai/AiPreferences.java
index a3ae3b2fefb..507e9fc8e92 100644
--- a/src/main/java/org/jabref/preferences/ai/AiPreferences.java
+++ b/src/main/java/org/jabref/preferences/ai/AiPreferences.java
@@ -335,6 +335,12 @@ public void setRagMinScore(double ragMinScore) {
      * @param runnable The runnable that should be executed when the preferences change.
      */
     public void addListenerToEmbeddingsParametersChange(Runnable runnable) {
+        customizeExpertSettings.addListener((observableValue, oldValue, newValue) -> {
+            if (newValue != oldValue) {
+                runnable.run();
+            }
+        });
+
         embeddingModel.addListener((observableValue, oldValue, newValue) -> {
             if (newValue != oldValue) {
                 runnable.run();