You need to understand how Preferences: (conversion section) works.
These are DEFAULTS for new, first time, conversions.
If a book has been converted, it remembers the settings used.
When you START any conversion, it shows any LAST USED settings. You can use that form to override those (there is also a clear option on the form, that will re-read the defaults)
Input and Output formats are also remembered, just change output to PDF
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