What takes a long time normally is for reviewers to write their review. We don't know if the PNAS will be sending the "new" paper back to the reviewers. Even if they are planning to do it the reviewers already know the paper they will have just to check the changes made so it should not take very long I would say.
I agree. I'm concerned about this. We know the paper had been reviewed, accepted for publication, and in galleys. We know it confirmed the WIP/NCI/Cleveland Clinic study.
Now the new version will be submitted in a few weeks - and needs to go through the "accepted/not-accepted" decision again.
Still feels fishy. Still a lot of potential for things to go wrong.