I updated my installer version and then took your suggestion, and it seems to have worked. I had to re-enable plugins, but their settings had been preserved. The file whose content had been deleted was restored (I may have made a trivial change to the file on another device between the onset of the problem and reconnecting to Sync; I’m not sure). Other settings seem OK. I haven’t yet checked if any other files are blank.
I’d love to know why this happened, but I doubt I’ll find out and for now the vault seems to be fixed.