Upgraded MySQL and accepted SSL/TLS Certs and now connection refused.

I have an active VPC Peering connection between 2 accounts where an EC2 instance on 1 account can connect to and use a RDS MySQL instance in the other. This has been working fine until I did 2 things and I'm not sure what the problem could now be.
When trying to connect to the RDS DB from the EC2 instance I now get this error:
ERROR 2003 (HY000): Can't connect to MySQL server on ......
The 2 actions I took lately where to upgrade the DB to 5.8.16 and accept and implement the update to Amazon RDS SSL/TLS certificates.
Does VPC Peering use SSL/TLS in a way that the change of these certs on the DB could be messing things up?