I am using the new beta version of Balsamiq (3.999.405 - 01/18/2017 13:40) and I think various parts of my mockup are disappearing as I move between screens. In my design I have a directory structure in a left hand sidebar. I have just come back to this screen and it has now disappeared. However, if you have a look at the Balsamiq thumbnail of this screen you will see the directory structure is still there. Sorry, not sure what actions made it disappear.
I wondered if my directory structure went to the background so I tried selecting all objects in this part of the mockup but nothing was selected. I am thus thinking it has been lost rather than hidden.