diff --git a/src/calibre/gui2/tag_view.py b/src/calibre/gui2/tag_view.py
index 72f0efd9bf..a64eb2eb9a 100644
--- a/src/calibre/gui2/tag_view.py
+++ b/src/calibre/gui2/tag_view.py
@@ -424,10 +424,8 @@ class TagsModel(QAbstractItemModel): # {{{
         self.categories = []
 
         # Reconstruct the user categories, putting them into metadata
+        self.db.field_metadata.remove_dynamic_categories()
         tb_cats = self.db.field_metadata
-        for k in tb_cats.keys():
-            if tb_cats[k]['kind'] in ['user', 'search']:
-                del tb_cats[k]
         for user_cat in sorted(self.db.prefs.get('user_categories', {}).keys()):
             cat_name = user_cat+':' # add the ':' to avoid name collision
             tb_cats.add_user_category(label=cat_name, name=user_cat)
diff --git a/src/calibre/gui2/ui.py b/src/calibre/gui2/ui.py
index 624935f279..1fc43116e6 100644
--- a/src/calibre/gui2/ui.py
+++ b/src/calibre/gui2/ui.py
@@ -523,11 +523,16 @@ class Main(MainWindow, MainWindowMixin, DeviceMixin, # {{{
 
     def shutdown(self, write_settings=True):
         try:
-            cf = self.library_view.model().db.clean
+            db = self.library_view.model().db
+            cf = db.clean
         except:
             pass
         else:
             cf()
+            # Save the current field_metadata for applications like calibre2opds
+            # Goes here, because if cf is valid, db is valid.
+            db.field_metadata.remove_dynamic_categories()
+            db.prefs['field_metadata'] = db.field_metadata.all_metadata()
         for action in self.iactions.values():
             if not action.shutting_down():
                 return
diff --git a/src/calibre/library/cli.py b/src/calibre/library/cli.py
index c17911cc3a..6b27021c2c 100644
--- a/src/calibre/library/cli.py
+++ b/src/calibre/library/cli.py
@@ -576,6 +576,9 @@ def command_add_custom_column(args, dbpath):
         return 1
     do_add_custom_column(get_db(dbpath, opts), args[0], args[1], args[2],
             opts.is_multiple, json.loads(opts.display))
+    # Re-open the DB so that  field_metadata is reflects the column changes
+    db = get_db(dbpath, opts)
+    db.prefs['field_metadata'] = db.field_metadata.all_metadata()
     return 0
 
 def catalog_option_parser(args):
@@ -799,6 +802,9 @@ def command_remove_custom_column(args, dbpath):
         return 1
 
     do_remove_custom_column(get_db(dbpath, opts), args[0], opts.force)
+    # Re-open the DB so that  field_metadata is reflects the column changes
+    db = get_db(dbpath, opts)
+    db.prefs['field_metadata'] = db.field_metadata.all_metadata()
     return 0
 
 def saved_searches_option_parser():
diff --git a/src/calibre/library/database2.py b/src/calibre/library/database2.py
index 05bab95ffe..cc4ddb1c17 100644
--- a/src/calibre/library/database2.py
+++ b/src/calibre/library/database2.py
@@ -290,10 +290,8 @@ class LibraryDatabase2(LibraryDatabase, SchemaUpgrade, CustomColumns):
 
         # Reconstruct the user categories, putting them into field_metadata
         # Assumption is that someone else will fix them if they change.
+        self.field_metadata.remove_dynamic_categories()
         tb_cats = self.field_metadata
-        for k in tb_cats.keys():
-            if tb_cats[k]['kind'] in ['user', 'search']:
-                del tb_cats[k]
         for user_cat in sorted(self.prefs.get('user_categories', {}).keys()):
             cat_name = user_cat+':' # add the ':' to avoid name collision
             tb_cats.add_user_category(label=cat_name, name=user_cat)
@@ -338,9 +336,6 @@ class LibraryDatabase2(LibraryDatabase, SchemaUpgrade, CustomColumns):
         setattr(self, 'title_sort', functools.partial(get_property,
                 loc=self.FIELD_MAP['sort']))
 
-        # Save the current field_metadata for applications like calibre2opds
-        self.prefs['field_metadata'] = self.field_metadata.all_metadata()
-
     def initialize_database(self):
         metadata_sqlite = open(P('metadata_sqlite.sql'), 'rb').read()
         self.conn.executescript(metadata_sqlite)
diff --git a/src/calibre/library/field_metadata.py b/src/calibre/library/field_metadata.py
index 449cb289ce..66cdee51f0 100644
--- a/src/calibre/library/field_metadata.py
+++ b/src/calibre/library/field_metadata.py
@@ -414,6 +414,12 @@ class FieldMetadata(dict):
             self._add_search_terms_to_map(key, [key])
             self.custom_label_to_key_map[label+'_index'] = key
 
+    def remove_dynamic_categories(self):
+        for key in list(self._tb_cats.keys()):
+            val = self._tb_cats[key]
+            if val['is_category'] and val['kind'] in ('user', 'search'):
+                del self._tb_cats[key]
+
     def cc_series_index_column_for(self, key):
         return self._tb_cats[key]['rec_index'] + 1