thanks for your comments daniel.

I've tried to reproduce this as well and couldn't either.
I started with a Xenial VM that had an older version of gnupg2 than 2.1 
installed.
I generated a key, and verified I could see it with both gpg and gpg2 as well 
as in seahorse.

I then upgraded to gnupg2 2.1 and checked with gpg2 --list-secret-keys
and the import process worked properly.

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https://bugs.launchpad.net/bugs/1565963

Title:
  gpg secret keys not migrated after upgrade to gnupg 2.1

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