While I don't know if my computer is failing and did recently make 43Mb of updates, I agree that it's possibly a tweak I did, because I changed many settings over the past few days. It would be hard to unravel them all. Instead here is some more information about the issue.
The file and application disappearing only happens when I open LibreOffice Calc files using links on the desktop or double click on the .ods file in my home folder, in either case when LibreOffice is closed. It doesn't happen if I open LibreOffice Calc first then open a .ods file from within LibreOffice; and it doesn't happen if I open LibreOffice first then open a .ods file using a link on the desktop or double click on a .ods file in my home folder. It doesn't happen for text files (Gedit), html files (Firefox), pdf files (Document Viewer) or jpeg files (Document Viewer or Gimp). None of the tweaks I did were to LibreOffice. I close applications after use so no other application is running.
If I first do a rogue action then a properly working action, I can tell from the opening speed that LibreOffice was already open, and when I look at the foot of the Window menu, the rogue file that disappeared off screen is listed, but if I click on its name, either nothing happens or the screen kind of slides to the side and I can see the rogue file. If I open the same file in both the rogue and working actions, the file's name appears twice, once accessibly and once either not or after the sliding phenomenon. If I close LibreOffice and open it again, the rogue file is still listed at the foot of the Window menu. If I restart the computer, a window flashes on the screen to tell me a process is still running and, although the restart proceeds before I can read the message, I can see that the message includes "LibreOffice" (although as far as I'm concerned LibreOffice is closed). Looking in System Monitor doesn't help me but maybe I don't know how to interpret what I see: most processes are described as "sleeping" and "LibreOffice" and "zeitgeist-datah" are described as "zombie" whichever way LibreOffice is opened.
I hoped someone could help me before I wrote an epic because when I start describing detail it's hard for me to stop and I get the notion that the detail may fog the issue. Let's hope not anyway.
Can anyone tell me what is happening here or suggest what I could try to do to change the rogue behaviour?