After today’s update, when logging into my EU account, all of my character progress, skins, etc. are gone. My account is now a level 0. What’s up with that?
Hi Windrunner!
It sounds like you’ve either logged into a different account, or logged into the wrong game region.
Can you check here and see if this helps please? 
I have almost exact same issue, I play both on EU and Americas, only American side was affected. All heroes wiped including free jaina from the tutorial. Level stayed the same though.
Edit: I have them all back again, I am sure I was logged into a correct realm, it had my level still intact. Weird bug, hope the OP got his issue resolved as well.