diff --git a/novelwriter/config.py b/novelwriter/config.py
index 404391b1..9258bcca 100644
--- a/novelwriter/config.py
+++ b/novelwriter/config.py
@@ -180,8 +180,8 @@ class Config:
         # Project Settings
         self.autoSaveProj    = 60     # Interval for auto-saving project, in seconds
         self.autoSaveDoc     = 30     # Interval for auto-saving document, in seconds
-        self.emphLabels      = True   # Add emphasis to H1 and H2 item labels
-        self.backupOnClose   = False  # Flag for running automatic backups
+        self.emphLabels      = False  # Add emphasis to H1 and H2 item labels
+        self.backupOnClose   = True   # Flag for running automatic backups
         self.askBeforeBackup = True   # Flag for asking before running automatic backup
         self.askBeforeExit   = True   # Flag for asking before exiting the app
 
@@ -208,7 +208,7 @@ class Config:
         self.doReplaceDash   = True     # Replace multiple hyphens with dashes
         self.doReplaceDots   = True     # Replace three dots with ellipsis
 
-        self.autoScroll      = False    # Typewriter-like scrolling
+        self.autoScroll      = True     # Typewriter-like scrolling
         self.autoScrollPos   = 30       # Start point for typewriter-like scrolling
         self.scrollPastEnd   = True     # Scroll past end of document, and centre cursor
 
diff --git a/novelwriter/core/coretools.py b/novelwriter/core/coretools.py
index a4b2a0b1..5113d8e7 100644
--- a/novelwriter/core/coretools.py
+++ b/novelwriter/core/coretools.py
@@ -609,6 +609,7 @@ class ProjectBuilder:
         project.data.setSaveCount(0)
         project.data.setAutoCount(0)
         project.data.setEditTime(0)
+        project.index.rebuild()
         project.saveProject()
         project.closeProject()
         return
diff --git a/tests/conftest.py b/tests/conftest.py
index 33baa870..a2c3ad03 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -39,6 +39,7 @@ from tests.mocked import MockGuiMain, MockTheme
 from tests.tools import cleanProject
 
 _TST_ROOT = Path(__file__).parent
+_SRC_ROOT = _TST_ROOT.parent
 _TMP_ROOT = _TST_ROOT / "temp"
 _TMP_CONF = _TMP_ROOT / "conf"
 
@@ -75,6 +76,8 @@ def sessionFixture():
     _TMP_ROOT.mkdir()
     _TMP_CONF.mkdir()
     (_TMP_ROOT / "manual.pdf").touch()
+    (_SRC_ROOT / "novelwriter" / "assets"/ "manual.pdf").touch()
+    (_SRC_ROOT / "novelwriter" / "assets"/ "manual_fr.pdf").touch()
     return
 
 
diff --git a/tests/reference/baseConfig_novelwriter.conf b/tests/reference/baseConfig_novelwriter.conf
index 8943a9b2..fa16b190 100644
--- a/tests/reference/baseConfig_novelwriter.conf
+++ b/tests/reference/baseConfig_novelwriter.conf
@@ -1,5 +1,5 @@
 [Meta]
-timestamp = 2025-06-02 16:21:38
+timestamp = 2025-06-10 23:18:12
 
 [Main]
 font = 
@@ -27,9 +27,9 @@ outlinepane = 500, 150
 [Project]
 autosaveproject = 60
 autosavedoc = 30
-emphlabels = True
+emphlabels = False
 backuppath = 
-backuponclose = False
+backuponclose = True
 askbeforebackup = True
 askbeforeexit = True
 lastauthor = 
@@ -49,7 +49,7 @@ repsquotes = True
 repdquotes = True
 repdash = True
 repdots = True
-autoscroll = False
+autoscroll = True
 autoscrollpos = 30
 scrollpastend = True
 fmtsquoteopen = ‘
@@ -91,3 +91,4 @@ searchmatchcap = False
 searchprojcase = False
 searchprojword = False
 searchprojregex = False
+
diff --git a/tests/test_dialogs/test_dlg_preferences.py b/tests/test_dialogs/test_dlg_preferences.py
index 1c54da98..9add0573 100644
--- a/tests/test_dialogs/test_dlg_preferences.py
+++ b/tests/test_dialogs/test_dlg_preferences.py
@@ -196,11 +196,11 @@ def testDlgPreferences_Settings(qtbot, monkeypatch, nwGUI, fncPath, tstPaths):
     # Project View
     prefs.iconColTree.setCurrentData("faded", "default")
     prefs.iconColDocs.setChecked(True)
-    prefs.emphLabels.setChecked(False)
+    prefs.emphLabels.setChecked(True)
 
     assert CONFIG.iconColTree == "theme"
     assert CONFIG.iconColDocs is False
-    assert CONFIG.emphLabels is True
+    assert CONFIG.emphLabels is False
 
     # Behaviour
     prefs.autoSaveDoc.stepUp()
@@ -261,11 +261,11 @@ def testDlgPreferences_Settings(qtbot, monkeypatch, nwGUI, fncPath, tstPaths):
 
     # Editor Scrolling
     prefs.scrollPastEnd.setChecked(False)
-    prefs.autoScroll.setChecked(True)
+    prefs.autoScroll.setChecked(False)
     prefs.autoScrollPos.stepUp()
 
     assert CONFIG.scrollPastEnd is True
-    assert CONFIG.autoScroll is False
+    assert CONFIG.autoScroll is True
     assert CONFIG.autoScrollPos == 30
 
     # Text Highlighting
@@ -362,7 +362,7 @@ def testDlgPreferences_Settings(qtbot, monkeypatch, nwGUI, fncPath, tstPaths):
     # Project View
     assert CONFIG.iconColTree == "faded"
     assert CONFIG.iconColDocs is True
-    assert CONFIG.emphLabels is False
+    assert CONFIG.emphLabels is True
 
     # Behaviour
     assert CONFIG.autoSaveDoc == 31
@@ -395,7 +395,7 @@ def testDlgPreferences_Settings(qtbot, monkeypatch, nwGUI, fncPath, tstPaths):
 
     # Editor Scrolling
     assert CONFIG.scrollPastEnd is False
-    assert CONFIG.autoScroll is True
+    assert CONFIG.autoScroll is False
     assert CONFIG.autoScrollPos == 31
 
     # Text Highlighting