diff --git a/cms/djangoapps/contentstore/management/commands/fix_not_found.py b/cms/djangoapps/contentstore/management/commands/fix_not_found.py
new file mode 100644
index 0000000000..392a72aa24
--- /dev/null
+++ b/cms/djangoapps/contentstore/management/commands/fix_not_found.py
@@ -0,0 +1,27 @@
+"""
+Script for fixing the item not found errors in a course
+"""
+from django.core.management.base import BaseCommand, CommandError
+from opaque_keys.edx.keys import CourseKey
+from xmodule.modulestore.django import modulestore
+from xmodule.modulestore import ModuleStoreEnum
+
+# To run from command line: ./manage.py cms fix_not_found course-v1:org+course+run
+
+
+class Command(BaseCommand):
+    """Fix a course's item not found errors"""
+    help = "Fix a course's ItemNotFound errors"
+
+    def handle(self, *args, **options):
+        "Execute the command"
+        if len(args) != 1:
+            raise CommandError("requires 1 argument: <course_id>")
+
+        course_key = CourseKey.from_string(args[0])
+        # for now only support on split mongo
+        owning_store = modulestore()._get_modulestore_for_courseid(course_key)
+        if hasattr(owning_store, 'fix_not_found'):
+            owning_store.fix_not_found(course_key, ModuleStoreEnum.UserID.mgmt_command)
+        else:
+            raise CommandError("The owning modulestore does not support this command.")
diff --git a/common/lib/xmodule/xmodule/modulestore/split_migrator.py b/common/lib/xmodule/xmodule/modulestore/split_migrator.py
index 8788e0679d..97191258ad 100644
--- a/common/lib/xmodule/xmodule/modulestore/split_migrator.py
+++ b/common/lib/xmodule/xmodule/modulestore/split_migrator.py
@@ -119,7 +119,7 @@ class SplitMigrator(object):
 
         # clean up orphans in published version: in old mongo, parents pointed to the union of their published and draft
         # children which meant some pointers were to non-existent locations in 'direct'
-        self.split_modulestore.internal_clean_children(course_version_locator)
+        self.split_modulestore.fix_not_found(course_version_locator, user_id)
 
     def _add_draft_modules_to_course(self, published_course_usage_key, source_course_key, user_id, **kwargs):
         """
diff --git a/common/lib/xmodule/xmodule/modulestore/split_mongo/split.py b/common/lib/xmodule/xmodule/modulestore/split_mongo/split.py
index 5cb62bcf57..3874d8d872 100644
--- a/common/lib/xmodule/xmodule/modulestore/split_mongo/split.py
+++ b/common/lib/xmodule/xmodule/modulestore/split_mongo/split.py
@@ -2418,22 +2418,26 @@ class SplitMongoModuleStore(SplitBulkWriteMixin, ModuleStoreWriteBase):
                 # update the index entry if appropriate
                 self._update_head(dest_course_key, index_entry, dest_course_key.branch, new_structure['_id'])
 
-    def internal_clean_children(self, course_locator):
+    def fix_not_found(self, course_locator, user_id):
         """
         Only intended for rather low level methods to use. Goes through the children attrs of
-        each block removing any whose block_id is not a member of the course. Does not generate
-        a new version of the course but overwrites the existing one.
+        each block removing any whose block_id is not a member of the course.
 
         :param course_locator: the course to clean
         """
         original_structure = self._lookup_course(course_locator).structure
-        for block in original_structure['blocks'].itervalues():
+        index_entry = self._get_index_if_valid(course_locator)
+        new_structure = self.version_structure(course_locator, original_structure, user_id)
+        for block in new_structure['blocks'].itervalues():
             if 'fields' in block and 'children' in block['fields']:
                 block['fields']["children"] = [
                     block_id for block_id in block['fields']["children"]
-                    if block_id in original_structure['blocks']
+                    if block_id in new_structure['blocks']
                 ]
-        self.update_structure(course_locator, original_structure)
+        self.update_structure(course_locator, new_structure)
+        if index_entry is not None:
+            # update the index entry if appropriate
+            self._update_head(course_locator, index_entry, course_locator.branch, new_structure['_id'])
 
     def convert_references_to_keys(self, course_key, xblock_class, jsonfields, blocks):
         """
diff --git a/common/lib/xmodule/xmodule/modulestore/split_mongo/split_draft.py b/common/lib/xmodule/xmodule/modulestore/split_mongo/split_draft.py
index 11b23295a4..77699fdd59 100644
--- a/common/lib/xmodule/xmodule/modulestore/split_mongo/split_draft.py
+++ b/common/lib/xmodule/xmodule/modulestore/split_mongo/split_draft.py
@@ -251,6 +251,16 @@ class DraftVersioningModuleStore(SplitMongoModuleStore, ModuleStoreDraftAndPubli
         course_key = self._map_revision_to_branch(course_key)
         return super(DraftVersioningModuleStore, self).get_orphans(course_key, **kwargs)
 
+    def fix_not_found(self, course_key, user_id):
+        """
+        Fix any children which point to non-existent blocks in the course's published and draft branches
+        """
+        for branch in [ModuleStoreEnum.RevisionOption.published_only, ModuleStoreEnum.RevisionOption.draft_only]:
+            super(DraftVersioningModuleStore, self).fix_not_found(
+                self._map_revision_to_branch(course_key, branch),
+                user_id
+            )
+
     def has_changes(self, xblock):
         """
         Checks if the given block has unpublished changes