If Charles the bold had a son he basically would have inherited everything, except for his sister's dowry.
However even with the situation of Charles the Bold only having a daughter, things were complicated. If you mean the entire Burgundian inheritance, various parts had their own inheritance laws.
Even the duchy of Burgundy wasn't that clear. IIRC The previous Capetian dukes of Burgundy had the right to succeeded by all their heirs simple (including women). When king John the Good of France succeeded in becoming duke of Burgundy, the duchy didn't merge with the crown of France, this was refused by the estates of Burgundy. John II finally gave the duchy of Burgundy to his youngest son Philip the Bold. However from this point on it was disputed whether the duchy of Burgundy was an appanage, obviously the kings of France were of the opinion that Burgundy was an appanage; in contrast the dukes of Burgundy began to argue, especially after the murder of John the Fearles that Burgundy wasn't an appanage. Reasons for this were the rights of previous dukes of Burgundy and the complex way how Burgundy was inherited. Although from a certain point there obviously also were political motives (which applies to both sides) on which way they choose the theory which suited them.