diff -r 99210fb3bc0a -r f08df4d38442 hgext/mq.py
--- a/hgext/mq.py	Mon Nov 22 16:05:31 2010 +0100
+++ b/hgext/mq.py	Tue Nov 16 13:06:07 2010 -0600
@@ -1295,12 +1295,18 @@
             # local dirstate. in this case, we want them to only
             # show up in the added section
             for x in m:
+                if x == '.hgsub' or x == '.hgsubstate':
+                    self.ui.warn(_('warning: not refreshing %s\n') % x)
+                    continue
                 if x not in aa:
                     mm.append(x)
             # we might end up with files added by the local dirstate that
             # were deleted by the patch.  In this case, they should only
             # show up in the changed section.
             for x in a:
+                if x == '.hgsub' or x == '.hgsubstate':
+                    self.ui.warn(_('warning: not adding %s\n') % x)
+                    continue
                 if x in dd:
                     del dd[dd.index(x)]
                     mm.append(x)
@@ -1310,6 +1316,9 @@
             # are not in the add or change column of the patch
             forget = []
             for x in d + r:
+                if x == '.hgsub' or x == '.hgsubstate':
+                    self.ui.warn(_('warning: not removing %s\n') % x)
+                    continue
                 if x in aa:
                     del aa[aa.index(x)]
                     forget.append(x)