diff -r 32a3860c799d -r e42cb31e9301 cubicweb/cwctl.py
--- a/cubicweb/cwctl.py	Tue Dec 15 08:35:13 2015 +0100
+++ b/cubicweb/cwctl.py	Thu Oct 22 16:58:12 2015 +0200
@@ -41,6 +41,7 @@
 from logilab.common.clcommands import CommandLine
 from logilab.common.shellutils import ASK
 from logilab.common.configuration import merge_options
+from logilab.common.decorators import clear_cache
 
 from cubicweb import ConfigurationError, ExecutionError, BadCommandUsage
 from cubicweb.cwconfig import CubicWebConfiguration as cwcfg, CWDEV, CONFIGURATIONS
@@ -749,6 +750,7 @@
             with mih.cnx:
                 with mih.cnx.security_enabled(False, False):
                     mih.migrate(vcconf, reversed(toupgrade), self.config)
+            clear_cache(config, 'instance_md5_version')
         else:
             print('-> no data migration needed for instance %s.' % appid)
         # rewrite main configuration file