Okay, I spoke with developers and it sounds like there is a known bug where Blueprints that depend on each other will cyclically mark other dirty, and that’s probably what’s happening here. This results in a UI bug where a blueprint can appear to be perpetually dirty (but it is just a UI bug). They’re working to fix that.
They wanted to check: If you turn Auto Recompile Blueprints back on, does this warning go away? It’s possible they need to stop marking things dirty in these situations if this option is turned off.