Hi Joe,
Thanks for the feedback. I was thinking something similar - where you could define layer "groups" that act like their own separate canvases and then for each operation you would specify which layer group to use to generate toolpaths from rather than just using the canvas in its state at the moment when you calculate the operation's toolpath. A layer would be able to belong to more than one group, etc.. It's something I've been kicking around and will keep it in mind :)
- Charlie