I’ve had two problems:
1 - my scratchpad files seemed to have disappeared.
2 - Scrivener stopped making back-ups (an error message appeared saying that Scriv had been unable to create the Zip file).
I’ve realised that both these things happened because I imported a set preferences made on another computer, that included locations for Scratchpad and Back-ups that do not exist on this computer.
Ok, so it was my bad for importinng preferences that didn’t work. But I feel that Scrivener should have been more helpful in alerting me to the problem, perhaps with a warning when the preferences were imported, and also with a more informative error message when the save failed.