You can recycle most of the things you make in this mod to their original components rather than nanites, there's no way to track which is which (to my knowledge), so it might be worthwhile to create a new entity with the same functionality so that you can't get unlimited steel/processing units/etc. as soon as you reach Neumann V.

I hadn't considered this. On first thought, I kind of like the emergent gameplay. Thank you for telling me, I'll think about this for a bit.

Oh I love the idea, but it might just be a bit too many resources since nanites are free :p