I have been having problems is Messages. One post suggested chucking your
login.keychain. This caused my secure notes to vanish.
Restoring this file from time machine (
~/Library/Keychains/login.keychain) did not help.
In answer to comment below:
Quit Keychain Access
Restored from the 7:31 backup this morning.
Restarted Keychain Access
No secure notes.
Mac OS 10.10 Yosemite