You could just disable the disk cache? Or at least flush it from the prefs?
I know, but doesn't that flush it for every project? I would love to keep the others, and just flush the current project's cache.
This is a known bug.
There is no way to flush the cache for just one project. It's all or nothing.
So, just as a tip, if you get a font error, before you hit 'ok' to continue, turn on your caps-lock, this will disable the rendering (and therefore the cache of it), close the project, and turn on the correct fonts, and re-open. That should work out fine.