Actually, at least from what I've read and researched, the territories inherited by Mary I from Charles the Bold hadn't change, it was after her death that Maximilian made a land exchange compromise with the French kings twice.
However I mostly about what would happen with Italy since (maybe?) Hapsburg interests in the area wouldn't be so large.
Yes they did change, France occupied the duchy of Burgundy (which France saw as an appanage, the Burgundian dukes had a different opinion (tradition in Burgundy (the original dukes had the right that allowed women to inherit in the absence of men); the way king John the Good of France also became duke of Burgundy, it explicitly refused to become a part of the French Crown), Picardie, the county of Artois, Franche Comté and the county of Charolais.
This conflict will have to be resolved; a part of the foreign policy of Habsburg Burgundy will be to get these territories back (IOTL emperor Charles V still wanted his entire Burgundian inheritance back); furthermore Burgundy proper could be disputed, but France's position was legally weaker in other territories (IOTL regained) with a tradition, which allowed women to inherit in the absence of men.
Armed conflict can enable some bending of the rules, but the situation after the death of Charles the Bold will lead to a Burgundian attempt of restoration.
Well Italy will be a part of the conflict, don't forget that the head of the Habsburg dynasty (usually) became the Holy Roman Emperor and the empire has it's own traditional position and ambition in Italy, Italy (formally) was a part of the Holy Roman Empire.
Furthermore the Habsburgs had their own ambitions in Northern Italy too and Milan also brings France closer to the Austrian Hereditary Lands.
Even without the Northern Italian ambitions of France, France had another major conflict with Aragon (later 'Spain') in Southern Italty regarding the kingdom of Naples. So given the fact that Habsburg-Burgundy and Trastamara 'Spain' both have a major conflict with France and thus share a common enemy, they become natural allies.
So IMO the Habsburg intrest in Italy, especially Northern Italy, wouldn't change much.