Well, I'll be honest. I stopped using it since I couldn't figure this out. You can easily fill your inventory up with the planners and the only way I could find to get rid of them is to throw them on the ground or toss them in a chest.
I have the same question. I'm in 0.16 and when I open up a plan, click the red trash can, the blueprint doesn't go away. I'm guessing this is a bug. Right now I'm just sticking them in my 'trash can' box.
Only way I found of getting rid of them permanently was to put extra planners in a cheap chest and destroy the chest. There should be a more seamless way of deleting/destroying extra planner items.
@LouisCyphre, that's the point. The interface is a little clunky and you end up creating extras that serve no purpose, and there's no good way to clean up that mess.