Maybe, although you might not have to go as far back as the Napoleonic Wars. See
this link. Apparently, there was supposed to be "Flemish and French parity" in the Congo, but French was favored from the beginning. This mirrors the linguistic situation in Belgium, where Flemish was stigmatized and French was used pretty exclusively in the public sphere. However, the very acknowledgment of Flemish in the charter means that there's at least a legal basis for a more widespread Flemish.
Despite that, there's still the issue that the colonial elites speak French, not Flemish. To circumvent that, you would need to have a large population of Dutch or Flemish speakers in the Congo. For instance, Leopold II could employ Dutch mercenaries to secure the Congo before the Belgian government takes over. These mercenaries could settle down and form a more local elite class. Maybe you could also get more Belgians to immigrate from Flanders as opposed to Wallonia. Flanders was much poorer, so there is a push factor; the issue is that the Congo is a lucrative colony, and as such, they would have to compete with profit-seeking Walloons to immigrate to the Congo. Another idea is that an increased presence of Flemish and Dutch missionaries could increase the profile of Flemish in the Congo. OTL there were plenty of Flemish missionaries, but they only spoke French in the churches. Dutch missionaries could help to raise the prestige of Dutch among the missionaries, meaning that Dutch/Flemish is more widely spoken by the missionaries, meaning that the average Congolese person will be more familiar with Dutch than French. All of these scenarios would result in a bilingual French/Dutch Congo, but the French aspect could be removed following independence, where some Mobutu analogue declares French to be an "elitist and colonial language" but keeps Dutch.
I'm just throwing out ideas, but basically I do think that Flemish could become more widespread in the Congo given some luck and the right POD, but the idea is large enough that it would probably require a separate thread to flesh it out. Getting back on topic, this would eliminate the Congo as a huge center of Francophone Africa, but unless other French colonies are butterflied, you would still have growing Francophone cities such as Abidjan to contend with.