Github user aljoscha commented on a diff in the pull request:

    https://github.com/apache/flink/pull/3535#discussion_r105956185
  
    --- Diff: 
flink-streaming-java/src/main/java/org/apache/flink/streaming/runtime/operators/windowing/WindowOperator.java
 ---
    @@ -354,22 +354,27 @@ public void merge(W mergeResult,
                                        }
                                });
     
    -                           // drop if the window is already late
    -                           if (isLate(actualWindow)) {
    -                                   
mergingWindows.retireWindow(actualWindow);
    -                                   continue;
    -                           }
    +                           context.key = key;
    +                           context.window = actualWindow;
     
                                W stateWindow = 
mergingWindows.getStateWindow(actualWindow);
                                if (stateWindow == null) {
                                        throw new IllegalStateException("Window 
" + window + " is not in in-flight window set.");
                                }
     
                                windowState.setCurrentNamespace(stateWindow);
    -                           windowState.add(element.getValue());
     
    -                           context.key = key;
    -                           context.window = actualWindow;
    +                           // Drop if the window is already late. In rare 
cases (with a misbehaving
    +                           // WindowAssigner) it can happen that a window 
becomes late that already has
    +                           // state (contents, state and timers). That's 
why we first get the window state
    +                           // above and then drop everything.
    +                           if (isLate(actualWindow)) {
    +                                   clearAllState(actualWindow, 
windowState, mergingWindows);
    +                                   mergingWindows.persist();
    --- End diff --
    
    The null check is not needed here since since we know from the if block 
we're in (`if (windowAssigner instanceof MergingWindowAssigner)`) that we do in 
fact have merging windows.
    
    Now that I look at it, though, I realise that the 
`mergingWindows.persist()` call is not necessary because we already call it at 
the end of the if block. So thanks for making me notice! 😃 
    
    I moved the call out of `clearAllState()` in the first place because all 
places where `clearAllState()` are called already persist afterwards. See, for 
example, `onEventTime()` and `onProcessingTime()`.



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