diff --git a/src/calibre/ebooks/oeb/parse_utils.py b/src/calibre/ebooks/oeb/parse_utils.py
index 5883241883..3fc37580bd 100644
--- a/src/calibre/ebooks/oeb/parse_utils.py
+++ b/src/calibre/ebooks/oeb/parse_utils.py
@@ -146,6 +146,15 @@ def clean_word_doc(data, log):
     return data
 
 
+def ensure_namespace_prefixes(node, nsmap):
+    namespace_uris = frozenset(nsmap.itervalues())
+    fnsmap = {k:v for k, v in node.nsmap.iteritems() if v not in namespace_uris}
+    fnsmap.update(nsmap)
+    if fnsmap != dict(node.nsmap):
+        node = clone_element(node, nsmap=fnsmap, in_context=False)
+    return node
+
+
 class HTML5Doc(ValueError):
     pass
 
@@ -307,11 +316,8 @@ def parse_html(data, log=None, decoder=None, preprocessor=None,
             nroot.append(elem)
         data = nroot
 
-    fnsmap = {k:v for k, v in data.nsmap.iteritems() if v != XHTML_NS}
-    fnsmap[None] = XHTML_NS
-    if fnsmap != dict(data.nsmap):
-        # Remove non default prefixes referring to the XHTML namespace
-        data = clone_element(data, nsmap=fnsmap, in_context=False)
+    # Remove non default prefixes referring to the XHTML namespace
+    data = ensure_namespace_prefixes(data, {None: XHTML_NS})
 
     data = merge_multiple_html_heads_and_bodies(data, log)
     # Ensure has a <head/>
diff --git a/src/calibre/ebooks/oeb/polish/upgrade.py b/src/calibre/ebooks/oeb/polish/upgrade.py
index 64859343cf..200634ca33 100644
--- a/src/calibre/ebooks/oeb/polish/upgrade.py
+++ b/src/calibre/ebooks/oeb/polish/upgrade.py
@@ -7,7 +7,8 @@ from __future__ import absolute_import, division, print_function, unicode_litera
 import sys
 
 from calibre.ebooks.metadata.opf_2_to_3 import upgrade_metadata
-from calibre.ebooks.oeb.base import OEB_DOCS, xpath
+from calibre.ebooks.oeb.base import EPUB_NS, OEB_DOCS, xpath
+from calibre.ebooks.oeb.parse_utils import ensure_namespace_prefixes
 from calibre.ebooks.oeb.polish.container import OEB_FONTS
 from calibre.ebooks.oeb.polish.opf import get_book_language
 from calibre.ebooks.oeb.polish.toc import (
@@ -36,8 +37,9 @@ def collect_properties(container):
             continue
         name = container.href_to_name(item.get('href'), container.opf_name)
         root = container.parsed(name)
+        root = ensure_namespace_prefixes(root, {'epub': EPUB_NS})
         properties = set()
-        container.dirty(name)  # Ensure entities are converted
+        container.replace(name, root)  # Ensure entities are converted
         if xpath(root, '//svg:svg'):
             properties.add('svg')
         if xpath(root, '//h:script'):