Figured it out. Sites have three options in the wp_options (or wp_n_options where n is the blog id) table. You can see them by running:
SELECT *
FROM wp_options
WHERE option_name IN ('current_theme', 'stylesheet', 'template')
To fix blogs after replacing a normal theme with a child theme of the same name, run an update on the wp_options table for that blog, setting the template option to the parent theme path:
UPDATE wp_options
SET option_value="parent-theme-path"
WHERE option_name="template";
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