In 1297, King Philippe IV the Fair attacked Flanders. But, in 1302, Flemish citizens rose and massacred the French occupation troops, defeated them in the battle of Kortrijk. The war went on until 1312, when Flanders and France made peace; Flanders ceded its French-speaking parts.
In 1336, an uprising happened in Flanders, directed against unpopular count Ludwig II under brewer Jakob van Artevelde. During this time, Flanders became a quasi-republic.
Flanders joined the first Aquitainian War on England's side, playing a vital role: For example, in the sea battle of Blankenberge 1344, English and Flemish defeated the French, so England now ruled the Channel and could land troops in Brittany. 1353, France had to make peace with England after the defeat in the battle of Caen. John of Montfort became duke of Brittany, England got all of Gascony (similar as in the peace of OTL 1360), and Flanders acquired the Artois.
Flanders also joined the second Aquitainian War. But in 1421, France made a separate peace with the Netherlands, giving Emperor Gerhard II of the HRE Flanders, which was incorporated into the Netherlands, and thus ceased to have its own history.
France would not give up its claim for Flanders, however. In the French-Dutch War of 1486-91, France took the Artois. In 1630-35, France and Denmark-Braunschweig fought the Netherlands in the Anti-Dutch War. In the peace of Bremen, the Dutch chose to keep their Caribbean colonies, giving Denmark-Braunschweig Nieuw-Nederland, and France got a good part of Flanders and all of Hennegau/Hainaut. As the Dutch say, now their Silver Age had also ended. After the anti-French War, however, the old borders of the Netherlands were restored.
After the Dutch War of Succession, France again took the disputed areas in 1729.