I have had exactly the same problem. I updated the Plugin in the last couple of days – can’t remember exactly.
I didn’t notice at first but this morning I thought something looked strange and it became apparent it had dissapeared! When I clicked on the Plugin tabs there was a message at the top saying it had been deactivated because the files had been deleted.
I was quite concerned but thankfully when I reinstalled it all the information I had filled in was still there.
I haven’t notice the Google ranking affected, but am obviously worried it may happen again for no reason. I have WP Security Audio Log installed and it doesn’t show anywhere that anybody deleted the file.