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The askyesno messagebox wrappers, added in #31287, returned None, which is interpreted as 'No', instead of the user entry. With 'Yes' not seen, nothing was saved.
The manual tests, once the problem was understood, is to save a new theme/keyset and click the delete button twice, clicking No the first time and Yes the second time, and see what happens.
Unit testing the current version of askyesno would be difficult since it calls messagebox.askyesno(), which returns an answer, and there is no obvious way to get a reference to the actual widget, in order to generate simulated key or click events.
A long term solution might be to add a new subclass to query.Query, after reviewing *it* for ease of testing.