Oh shoot your right! hmm
They would probably have to split those thrones though.
Nah they wouldn't. Co Flanders and Du Burgundy are fiefs of the Crown of France in the 15th C they would be reunited with the Royal Demesne. The remainder would be held by the King of France as fiefs of the Empire. Which gives them a real and very influential stake in any future Imperial Election.
however, had House Valois-Burgundy passed through the female line, say Mary the Rich, pity the marriage plans of Nicholas of Lorraine did not come to fruition, uniting Lorraine and Bar with the rest of the Burgundian collection then they would have formed a continuous block (without allies its doubtful that Nicholas would have been as successful as Maximilian it should be noted). The V-B might still have the senior male heir, but not the Senior heir- general. Those would still be Claude and Margaret, provided one of their husbands has a claim on the crown as well, then they would probably inherit...or more properly their husband would be accepted as heir. That could still leave the throne to the Bourbons. However, the continuing existence of the House V-B, or even Valois-Vaudémont, would almost certainly have intermarried again back into the main line. Say Claude for instance instead of taking husband from the Vaudémont of Lorraine but instead from Valois-Vaudémont of Burgundy-Lorraine instead, then they would probably still gain the throne instead of Bourbon. Claude being elder to Margaret, and the Valois-Vaudémont having a male line claim at least as good as the Bourbon once you factor in the likely political factions in play and Religion. Bourbon was Huguenot protestant.. Valois-Vaudémont would probably remain Catholic but tolerant from necessity.