diff --git a/src/calibre/gui2/ui.py b/src/calibre/gui2/ui.py
index 1e7c7550f8..2082a3b90a 100644
--- a/src/calibre/gui2/ui.py
+++ b/src/calibre/gui2/ui.py
@@ -565,6 +565,9 @@ class Main(MainWindow, MainWindowMixin, DeviceMixin, # {{{
         mb = self.library_view.model().metadata_backup
         if mb is not None:
             mb.stop()
+            # give the thread time to stop so all operations complete
+            # otherwise the exit could kill the thread mid-write
+            time.sleep(2)
 
         self.hide_windows()
         self.emailer.stop()
diff --git a/src/calibre/library/caches.py b/src/calibre/library/caches.py
index 7a15cb3ce1..09adc4a9fd 100644
--- a/src/calibre/library/caches.py
+++ b/src/calibre/library/caches.py
@@ -39,6 +39,7 @@ class MetadataBackup(Thread): # {{{
         self.do_write = FunctionDispatcher(self.write)
         self.get_metadata_for_dump = FunctionDispatcher(db.get_metadata_for_dump)
         self.clear_dirtied = FunctionDispatcher(db.clear_dirtied)
+        self.set_dirtied = FunctionDispatcher(db.dirtied)
 
     def stop(self):
         self.keep_running = False
@@ -68,8 +69,9 @@ class MetadataBackup(Thread): # {{{
                     traceback.print_exc()
                     continue
 
+            # at this point the dirty indication is off
+
             if mi is None:
-                self.clear_dirtied([id_])
                 continue
 
             # Give the GUI thread a chance to do something. Python threads don't
@@ -79,6 +81,7 @@ class MetadataBackup(Thread): # {{{
             try:
                 raw = metadata_to_opf(mi)
             except:
+                self.set_dirtied([id_])
                 prints('Failed to convert to opf for id:', id_)
                 traceback.print_exc()
                 continue
@@ -92,16 +95,11 @@ class MetadataBackup(Thread): # {{{
                 try:
                     self.do_write(path, raw)
                 except:
+                    self.set_dirtied([id_])
                     prints('Failed to write backup metadata for id:', id_,
                             'again, giving up')
                     continue
 
-            time.sleep(0.1) # Give the GUI thread a chance to do something
-            try:
-                self.clear_dirtied([id_])
-            except:
-                prints('Failed to clear dirtied for id:', id_)
-
     def write(self, path, raw):
         with open(path, 'wb') as f:
             f.write(raw)
diff --git a/src/calibre/library/database2.py b/src/calibre/library/database2.py
index ce72b473e1..281f8cdc78 100644
--- a/src/calibre/library/database2.py
+++ b/src/calibre/library/database2.py
@@ -598,20 +598,17 @@ class LibraryDatabase2(LibraryDatabase, SchemaUpgrade, CustomColumns):
         for book_id in book_ids:
             if not self.data.has_id(book_id):
                 continue
-            path, mi = self.get_metadata_for_dump(book_id)
+            path, mi = self.get_metadata_for_dump(book_id,
+                                        remove_from_dirtied=remove_from_dirtied)
             if path is None:
                 continue
-            raw = metadata_to_opf(mi)
-            with open(path, 'wb') as f:
-                f.write(raw)
-            if remove_from_dirtied:
-                self.conn.execute('DELETE FROM metadata_dirtied WHERE book=?',
-                        (book_id,))
-                # if a later exception prevents the commit, then the dirtied
-                # table will still have the book. No big deal, because the OPF
-                # is there and correct. We will simply do it again on next
-                # start
-                self.dirtied_cache.discard(book_id)
+            try:
+                raw = metadata_to_opf(mi)
+                with open(path, 'wb') as f:
+                    f.write(raw)
+            except:
+                # Something went wrong. Put the book back on the dirty list
+                self.dirtied([book_id])
         if commit:
             self.conn.commit()
         return True
@@ -649,7 +646,7 @@ class LibraryDatabase2(LibraryDatabase, SchemaUpgrade, CustomColumns):
         self.dirtied_cache = set()
         self.dirtied(book_ids)
 
-    def get_metadata_for_dump(self, idx):
+    def get_metadata_for_dump(self, idx, remove_from_dirtied=True):
         try:
             path = os.path.join(self.abspath(idx, index_is_id=True), 'metadata.opf')
             mi = self.get_metadata(idx, index_is_id=True)
@@ -658,7 +655,18 @@ class LibraryDatabase2(LibraryDatabase, SchemaUpgrade, CustomColumns):
             # cover is set/removed
             mi.cover = 'cover.jpg'
         except:
-            return (None, None)
+            # This almost certainly means that the book has been deleted while
+            # the backup operation sat in the queue.
+            path,mi = (None, None)
+
+        try:
+            # clear the dirtied indicator. The user must put it back if
+            # something goes wrong with writing the OPF
+            if remove_from_dirtied:
+                self.clear_dirtied([idx])
+        except:
+            # No real problem. We will just do it again.
+            pass
         return (path, mi)
 
     def get_metadata(self, idx, index_is_id=False, get_cover=False):