That isn't quite correct. The per book settings are only stored in the database if you open the font settings and make a change. Once you do that, whenever you open that book, it will open with those settings. Those settings are written to the configuration file and used as the default for other books.
Agreed. Another way of stating it is that if you then change the default size a second time, the new default applies to new books opened, but not to the earlier one where you changed the size. The size in any given book "sticks" even if you subsequently change the default.
This supports GeoffR's observation that changing the default externally did not change the book with which he was having the problem, making him think that the default change "didn't work".