Paratext can only automatically sort glossary entries that are properly linked in the Biblical terms tool. Changing the spelling of a citation form in the glossary breaks the link in the Biblical terms tool. You will have to open the Biblical terms tool and re-link the citation form to the Biblical term. You can verify that glossary citation form is linked to the Biblical term by looking for an asterisks on the glossary tab in the Biblical terms tool.
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If there is no asterisks, then link the term by doing the following steps:
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Paratext will now correctly sort that glossary entry using the sort order in your projects language settings. Repeat this process for all entries that have changed and are no longer being sorted correctly.