Flynn does self-heal after node reboots, so if that is not working for you then it is a bug we need to fix.
When you do have issues it would be really helpful to us and other users if you could open a GitHub issue or come and chat to us in IRC (#flynn on Freenode) so we can fix any bugs you are encountering. I fully understand you just want to be concentrating on building your product, this is why we are building Flynn!