Even if your race won’t have too many VO2 max efforts in it, over the course of 24hrs, you’re certainly going to rack up plenty of time in that zone. You’ll also still be training and preparing your body for the demands of your event, and fitness from each zone you train has crossover with the other zones you’ll be riding in. We’d recommend trying to stick with your VO2 workouts if that’s possible.
We’d also strongly advise seeing a physiotherapist/expert when it comes to knee pain like this. It’s tough to get to the bottom of these issues on the internet. We do have a lengthy Forum thread on this subject from the past that might be worth taking a look at – but if your knee pain persists, seeking professional help would be the right move!