Currently comint.el does not respect local values of comint-input-ring-separator. Sql mode on the other hand sets it locally. This prevents multi-line sql history from working.

Sql history is stored using comint-write-input-ring. When it saves the history file, it uses with-current-buffer, thus ignoring previous local value. When read comint-read-input-ring uses with-temp-buffer with similar results.

This seems to have been caused by the fix for this bug.

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Best Regards,
Nikolay Kudryavtsev