Why have all my custom Civi fields stopped showing up in Drupal view?
In most cases this is fixed by running drush cc all. I don't know what the circumstances are that causes the upgrading 'clear caches' to not suffice but this seems to be the fix.

If 'Clear Caches' does not suffice you could also try Structure > Views > Settings > Advanced, Clear Views' cache but I have never needed to do that.