As a result of the fix for
NIFI-2032, previously enabled ControllerServices become disabled after a restart if they are not referenced by another component. However, we use a custom domain specific langauge that can reference a controller service from a query defined as a custom processor's property. This means that we use a number of controller service that are only used in this way (i.e. are never directly referred to by another component). Upon restart, these are now disabled causing issues with our flows.
I have not yet stepped through the new enableControllerServices()  method to figure out exactly where the issue is coming from, but I wanted to get the ticket out there and on the radar, as this breaks backwards compatibility on a feature we heavily rely on.