Philibert II of Savoy: Not childless

Margaret of Austria was Catherine of Aragon's sister-in-law.
Margaret married the Infante Juan (John), the only son of Ferdinand and Isabella. Juan died in 1497. He and Margaret had no children.
Margaret married Philibert II, Duke of Savoy in 1501.
Philibert died in September of 1504. He and Margaret had no children.
Suppose Philibert II and Margaret have these children:
Amadeus born 1502
Yolande born 1504
What happens then?
 
Amadeus (born 1502) shall become Amadeus IX, Duke of Savoy.
Margaret, Dowager Duchess of Savoy is the regent.
Does Margaret's father, Holy Roman Emperor Maximilian I still name her governor of the Low Countries in 1507?
 
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