over in https://bugs.launchpad.net/bugs/1565963, we have a documented situation
where ~/.gnupg/private-keys-v1.d is not executable for the user, and as a
result, the migration process fails.
Even worse, it appears to succeed, because ~/.gnupg/.gpg-v21-migrated is created.
This means that subsequent use of GnuPG 2.1 simply can't find the secret keys,
even though they're available in ~/.gnupg/secring.gpg
Please see further discussion over here: