The removal of this feature was both surprising and jarring for me. It has caused a chilling affect to how I think about Evernote now. I don't think that Evernote realized that this was not just a search function, but an organizational function for many users. I would intentionally take notes in places to help with organization. I had (still have) a "Fieldnotes" notebook with location based notes that I referenced when I travel. It was such an amazing feeling to be able to see where notes had been taken. I was building my own Guide, like from HGTTG. Because of the removal of Atlas, I've essentially "lost data." Yes the metadata is still there, but it's useless.
I'm glad to see that this thread is still seeing some interest. Keep hitting that up vote button.
I also started a Quora thread and there might be some new information for people there. https://www.quora.com/Why-did-Evernote-remove-the-Atlas-feature