First, put a lot of fresh water in the bowl and flush it. Jeanneau actually has what seems like a good design here. They use a second joker valve above the standard toilet one. This is supposed to lower the pressure on the toilet joker but also means when you disconnect the hose at the toilet then you don't get the whole pipe contents spilling on the floor.
Anyway to cut a long story short, the valve were pretty easy to swap out but a little boat yoga is required as the screws are tricky to get at. The replacement joker valves worried me as I'd read that if you can see any light through them at all then get them replaced but both jabsco and Defender.com both said that's rubbish and I gotta say after 2 weeks of using the valves that I could see through that they are right. The toilet backflow is much improved. The valves I took out had maybe 1/4 inch of a gap, and the new ones looked much better.
The toilets basically are fixed. I come back to the boat now and the toilet water is the correct color :)
Standard valve on bottom.