I guess in theory you could modify or leave the fp out of the plans, but I don't see how they would be accurate anymore even if u ignored those parts.
The plans worked because they understood that x number of people were normally in a certain part of the park at a certain time. Then they moved you to the parts of the park with the least amount of people. Since the old fp effected where those crowds built and when, none of that applies now.
I expect we will start seeing new crowds and lines in new places. Eventually, the plans will be a big time saver again, but I don't see that happening until new data is collected. You have to remember they had years of data and real world testing put into computer algorithms to create the current plans, now it's a whole new game.
I kind of feel bad for them. It's going to be almost like starting over. They will need to collect all new data to figure out where people are going when with the new system. Add to that, that the old fp has been gradually phased out. No one will be able to collect any valid data until the old system is completely gone and people have had a chance to settle into whatever the new patterns turn into. Once those new patterns are established, they will be able to feed that data into the computer and create new plans that work with the new system, but I wouldn't expect to see those turn up for quite a while.
I actually expect new plans may make the whole situation worse with plans telling people book XY&Z as your FP+ choices, then ride AB&C, with everyone trying to do the same thing at the same time. Because there is really no other way to fit it all in, since you can't pull throughout the day like before. Many people who wouldn't bother to follow a plan before, will now at least follow the first part of the instructions to book XY&Z because what does that cost them? They won't need to get up early, or stick to a plan, so if the guide book says book these specific FP+, I think people will try to do it.
It should be interesting to see what happens.