So you're likely using Cypher 2.0, and looking at your query, you don't have a MATCH--just a START and a RETURN. So, first off, I'm not even sure that's legal, but you say it ran before...I've never seen that. :)
That said, I'm pretty sure that the START clause makes use of legacy indices, and it looks like you're attempting to treat :User as a label (which is new to Neo4j 2.x). So, when SDN creates the schema indices (with "name" and "email" as your keys), the START statement is attempting to access a legacy index for "User" which does not exist.
Maybe try this as a query and let us know how it goes:
MATCH (n:User {email: <whatever>}) RETURN count(*);
Also make sure that your parameterization is being taken care of.
(If I'm off on any of this, someone please feel free to correct me.)
HTH