I think I kinda broke the Burgundian Succession

I'm playing as Burgundy and when Charles died I chose to become a PU of France to inherit all my vassals (including France's starting vassals which I aquired through missions).

But just a month after his death Mary also died, that event started an Independence War, which I quickly won. But I think you are not supposed to gain independence in the year the Imperial Incident is active. The Emperor chose to demand the Lowlands but I never got any popup about that and looking through the wiki, there are multiple events for Burgundy's overlord (no alternatives if there isn't any overlord) and only those clear the flag 'burgundian_succession_start' and set the flag 'bur_crisis_has_happened'. Through melting my savestate I confirmed I have the flag 'burgundian_succession_start' active.

For most of the gameplay that is not that relevant that I'm an independent Burgundy with a never cleared flag but there is one mission, 'Secure the Succession', which adds me and all my provinces to the HRE when that flag is not cleared. If I don't have that flag active I can get an event to get Subjugation/PU CBs on all electors, which I would much prefer.

So is there any way to clear that flag if I'm already independent? I have one backup save from when I'm still in the Incident and Mary is still alive but I would much prefer not to use that.