diff --git a/main.lua b/main.lua
index a7839f5..ca277da 100644
--- a/main.lua
+++ b/main.lua
@@ -84,7 +84,28 @@ function Bookhoard:init()
         self:updateProgress(false, false)
     end
 
-    self.settings = G_reader_settings:readSetting(self.settings_key, self.default_settings)
+    -- readSetting returns the STORED table verbatim when one exists — it
+    -- does not merge defaults. A settings file saved by an older plugin
+    -- version lacks the annotation toggles entirely, so sync_bookmarks/
+    -- highlights/notes read as nil, the "or" in _doUpdateProgress fell
+    -- through to the else branch, and every push carried EMPTY annotation
+    -- arrays while progress synced fine. Merge missing defaults (and
+    -- persist once so the file and the menu checkboxes self-heal).
+    self.settings = G_reader_settings:readSetting(self.settings_key, {})
+    if type(self.settings) ~= "table" then
+        self.settings = {}
+    end
+    local settings_merged = false
+    for key, value in pairs(self.default_settings) do
+        if self.settings[key] == nil then
+            self.settings[key] = value
+            settings_merged = true
+        end
+    end
+    if settings_merged then
+        G_reader_settings:saveSetting(self.settings_key, self.settings)
+        logger.info("Bookhoard: merged new default settings (older settings file)")
+    end
 
     if self.settings.auto_sync
         and Device:hasSeamlessWifiToggle()