diff -r 9b4de34ad394 -r 97095348b3ee cubicweb/server/sources/native.py
--- a/cubicweb/server/sources/native.py	Thu Feb 11 21:59:49 2016 +0100
+++ b/cubicweb/server/sources/native.py	Wed Feb 17 13:45:34 2016 +0100
@@ -43,7 +43,7 @@
 
 from logilab.common.decorators import cached, clear_cache
 from logilab.common.configuration import Method
-from logilab.common.shellutils import getlogin
+from logilab.common.shellutils import getlogin, ASK
 from logilab.database import get_db_helper, sqlgen
 
 from yams.schema import role_name
@@ -56,7 +56,7 @@
 from cubicweb.cwconfig import CubicWebNoAppConfiguration
 from cubicweb.server import hook
 from cubicweb.server import schema2sql as y2sql
-from cubicweb.server.utils import crypt_password, eschema_eid, verify_and_update
+from cubicweb.server.utils import crypt_password, verify_and_update
 from cubicweb.server.sqlutils import SQL_PREFIX, SQLAdapterMixIn
 from cubicweb.server.rqlannotation import set_qdata
 from cubicweb.server.hook import CleanupDeletedEidsCacheOp
@@ -915,17 +915,14 @@
                  'asource': text_type(source.uri)}
         self._handle_insert_entity_sql(cnx, self.sqlgen.insert('entities', attrs), attrs)
         # insert core relations: is, is_instance_of and cw_source
-        try:
+
+        if entity.e_schema.eid is not None:  # else schema has not yet been serialized
             self._handle_is_relation_sql(cnx, 'INSERT INTO is_relation(eid_from,eid_to) VALUES (%s,%s)',
-                                         (entity.eid, eschema_eid(cnx, entity.e_schema)))
-        except IndexError:
-            # during schema serialization, skip
-            pass
-        else:
+                                         (entity.eid, entity.e_schema.eid))
             for eschema in entity.e_schema.ancestors() + [entity.e_schema]:
                 self._handle_is_relation_sql(cnx,
                                              'INSERT INTO is_instance_of_relation(eid_from,eid_to) VALUES (%s,%s)',
-                                             (entity.eid, eschema_eid(cnx, eschema)))
+                                             (entity.eid, eschema.eid))
         if 'CWSource' in self.schema and source.eid is not None: # else, cw < 3.10
             self._handle_is_relation_sql(cnx, 'INSERT INTO cw_source_relation(eid_from,eid_to) VALUES (%s,%s)',
                                          (entity.eid, source.eid))
@@ -1742,15 +1739,20 @@
         tables = archive.read('tables.txt').splitlines()
         sequences = archive.read('sequences.txt').splitlines()
         numranges = archive.read('numranges.txt').splitlines()
-        file_versions = self._parse_versions(archive.read('versions.txt'))
-        versions = set(self._get_versions())
-        if file_versions != versions:
-            self.logger.critical('Unable to restore : versions do not match')
-            self.logger.critical('Expected:\n%s', '\n'.join('%s : %s' % (cube, ver)
-                                                            for cube, ver in sorted(versions)))
-            self.logger.critical('Found:\n%s', '\n'.join('%s : %s' % (cube, ver)
-                                                         for cube, ver in sorted(file_versions)))
-            raise ValueError('Unable to restore : versions do not match')
+        archive_versions = self._parse_versions(archive.read('versions.txt'))
+        db_versions = set(self._get_versions())
+        if archive_versions != db_versions:
+            self.logger.critical('Restore warning: versions do not match')
+            new_cubes = db_versions - archive_versions
+            if new_cubes:
+                self.logger.critical('In the db:\n%s', '\n'.join('%s: %s' % (cube, ver)
+                                                            for cube, ver in sorted(new_cubes)))
+            old_cubes = archive_versions - db_versions
+            if old_cubes:
+                self.logger.critical('In the archive:\n%s', '\n'.join('%s: %s' % (cube, ver)
+                                                            for cube, ver in sorted(old_cubes)))
+            if not ASK.confirm('Versions mismatch: continue anyway ?', False):
+                raise ValueError('Unable to restore: versions do not match')
         table_chunks = {}
         for name in archive.namelist():
             if not name.startswith('tables/'):