Legally speaking, the lands of the dukes of Burgundy fell into four categories :
1. Apanages : lands from the royal french demesne conceded to a younger son of a king. Here, the duchy of Burgundy. Normally, the concession of the apanage has a clause in which the apanage comes back to the king in case the male line of the first grantee comes extinct. The Burgundian concession had no such clause, but the kings' lawyers can always argue it is a non-written rule. The Picardian cities are very close to this category, as it is a part of the royal demesne given by treaty to the Duke, with restricting clauses regarding the succession.
2. Territories held in fief from the french king. Here, the counties of Rethel, Nevers, Artois, Flanders, Charolais, Maconnais, Eu, Boulogne, Vermandois. They follow their own inheritance laws (usually male-preference primogeniture), but the king can always declare the duke a felon and confiscate his fiefs. This is known as the "commise féodale" or "Philip Augustus' method of management".
3. Territories held in fief from the Emperor. The Duchies of Brabant, Luxembourg, Limburg, counties of Hainaut, Burgundy, Namur, Holland, Zealand. The emperor's intervention, while possible in theory, is very unlikely.
4. Territories under influence. The Duke does not own them, but he have enough influence on the local lord to rule them. Bishoprics of Liege, Utrecht, Toul, Metz, Verdun and Duchy of Guelders.
Historically, no french king ever confiscated the apanage of one of the princes when the line of succession is unbroken. The closest example is the Artois case, in the 1310', when the male-heir (but not the son of his predecessor) of the Artois line, Robert, was deprived of the major part of his inheritance to a closer, female heir, who happened to be Philip V's mother-in-law ! Same for the Bourbon case in the 1520'. If the King sees an opening (for example, a duke being sonless, but with a nephew as designated heir), he might confiscate ducal Burgundy and Picardy cities, but with a continuing line of Valois in Burgundy, he simply cannot act.
The more useful example could be Louis of Orléans (Louis XII), after his rebellion in 1488 in the "Mad War", his lands (apanage+fiefs) were confiscated as he was kept in prison awaiting formal trial. In 1491, he was granted a pardon, and his lands restored to him. ITTL, the King of France could kept a duke of Burgundy in prison the longest time possible and kept his lands under his arm "awaiting trial", but depriving a legal heir of his birthright is the red line for the aristocracy.