Hi Shane,
I am having the same issue - I have been trying to sync for several days now. The web app and the desktop (Windows 10) app are in sync. Everything there works.
Unfortunately, however, the iOS app has my old structure and apps from years ago and will not update. Nothing I can do will update it. I’ve tried sign in/out, going through the logs, but it seems to be an issue with the sync master. Specifically, the logs mention an issue with an indexingtree or something like that.
I am frustrated because I just rejoined Evernote after years of not using the service and was excited to see what’s new. Instead, I find this really, really buggy mess and I am struggling to find the value I am paying for.
I know its not your fault Shane but I hope the development team are aware of the issues and the gravity of the issues.
Thank you.