So I looked over everything, and it looks like my desktop version (on windows 10 enterprise) sync has failed. Error 19416 & 15716 can't connect to server. Tried the troubleshooting options but to no avail. It does look like my work has suddenly banned Evernote, as even the website is blocked, so I'm assuming firewall settings were changed. It doesn't completely explain out of org emails not showing up in the sync but it's probably to do with that.
Thanks for your help though, if you have any suggestions for the sync issue just let me know as the company ICT department might as well be a Wendy's.