diff --git a/src/calibre/ebooks/metadata/epub.py b/src/calibre/ebooks/metadata/epub.py
index 8894362766..1ad12a915a 100644
--- a/src/calibre/ebooks/metadata/epub.py
+++ b/src/calibre/ebooks/metadata/epub.py
@@ -277,20 +277,9 @@ def update_metadata(opf, mi, apply_null=False, update_timestamp=False, force_ide
     if mi.languages:
         mi.languages = normalize_languages(list(opf.raw_languages) or [], mi.languages)
 
-    opf.smart_update(mi)
+    opf.smart_update(mi, apply_null=apply_null)
     if getattr(mi, 'uuid', None):
         opf.application_id = mi.uuid
-    if apply_null:
-        if not getattr(mi, 'series', None):
-            opf.series = None
-        if not getattr(mi, 'tags', []):
-            opf.tags = []
-        if not getattr(mi, 'isbn', None):
-            opf.isbn = None
-        if not getattr(mi, 'comments', None):
-            opf.comments = None
-        if not getattr(mi, 'publisher', None):
-            opf.publisher = None
     if apply_null or force_identifiers:
         opf.set_identifiers(mi.get_identifiers())
     else:
diff --git a/src/calibre/ebooks/metadata/opf2.py b/src/calibre/ebooks/metadata/opf2.py
index 7b71e03cc1..10ac69ac73 100644
--- a/src/calibre/ebooks/metadata/opf2.py
+++ b/src/calibre/ebooks/metadata/opf2.py
@@ -1249,19 +1249,46 @@ class OPF(object):  # {{{
             raw = '<?xml version="1.0"  encoding="%s"?>\n'%encoding.upper()+raw
         return raw
 
-    def smart_update(self, mi, replace_metadata=False):
+    def smart_update(self, mi, replace_metadata=False, apply_null=False):
         for attr in ('title', 'authors', 'author_sort', 'title_sort',
                      'publisher', 'series', 'series_index', 'rating',
                      'isbn', 'tags', 'category', 'comments', 'book_producer',
                      'pubdate', 'user_categories', 'author_link_map'):
             val = getattr(mi, attr, None)
-            if val is not None and val != [] and val != (None, None):
+            is_null = val is None or val in ((), [], (None, None), {})
+            if is_null:
+                if apply_null and attr in {'series', 'tags', 'isbn', 'comments', 'publisher'}:
+                    setattr(self, attr, ([] if attr == 'tags' else None))
+            else:
                 setattr(self, attr, val)
         langs = getattr(mi, 'languages', [])
         if langs and langs != ['und']:
             self.languages = langs
         temp = self.to_book_metadata()
         temp.smart_update(mi, replace_metadata=replace_metadata)
+        if not replace_metadata and callable(getattr(temp, 'custom_field_keys', None)):
+            # We have to replace non-null fields regardless of the value of
+            # replace_metadata to match the behavior of the builtin fields
+            # above.
+            for x in temp.custom_field_keys():
+                meta = temp.get_user_metadata(x, make_copy=True)
+                if meta is None:
+                    continue
+                if meta['datatype'] == 'text' and meta['is_multiple']:
+                    val = mi.get(x, [])
+                    if val or apply_null:
+                        temp.set(x, val)
+                elif meta['datatype'] in {'int', 'float', 'bool'}:
+                    missing = object()
+                    val = mi.get(x, missing)
+                    if val is missing:
+                        if apply_null:
+                            temp.set(x, None)
+                    elif apply_null or val is not None:
+                        temp.set(x, val)
+                elif apply_null and mi.is_null(x) and not temp.is_null(x):
+                    temp.set(x, None)
+
         self._user_metadata_ = temp.get_all_user_metadata(True)
 
 # }}}