Building on top of bugs:
I tried to stop a Flink application on YARN via savepoint which didn't succeed due to a possible bug/racecondition in shutdown (Bug 21028). Due to some reason, Flink attempted to restart the pipeline after the failure in shutdown (21029). The bug here:
As I mentioned: My jobgraph is disjoint and the pipelines are fully isolated. Lets say the original error occured in a single task of pipeline1. Flink then restarted the entire pipeline1, but pipeline2 was shutdown successfully and switched the state to FINISHED.
My job thus was in kind of an invalid state after the attempt to stopping: One of two pipelines was running, the other was FINISHED. I guess this is kind of a bug in the restarting behavior that only all connected components of a graph are restarted, but the others aren't...