[Quoth]

I'll investigate further. The Book Check thing in Editor does seem to rename the CSS as well as the file. I'd expect those to have to match. So I may be doing something subtly wrong on the occasions it doesn't work.

Edit:
Right now I don't seem to be able to recreate the issue.
I see that if you try to quit the Editor without saving there is a warning about saving changed files. But the fonts are ALREADY renamed. So if you forget the editor is open and send the epub to the Kobo, then the CSS is original. Hence quite reasonably there is some brokenness.

So I will click on Save always straight after letting the Check tool rename the fonts. Hopefully I won't see this problem ever again. Though I'm only guessing that it's what I've done wrong occasionally.