Thanks for sharing the example – I'll try it out and have a look.
As I mentioned above, annotating pre-defined spans in the manual interface is not "officially" supported in Prodigy v1.2.0 – so everything you're doing here is pretty experimental and may not work perfectly. The updated interface and new ner.make-gold workflow coming in v1.3.0 will implement all of the required changes in the core library, so you'll be able to use this workflow out-of-the-box.