blowing dust off thread 
I actually found a solution (which took me some days to get my head around) in the Lyra sample project 
You need to register the Gameplay Cues that are not inside your main content (typically Content/GameplayCues), e.g. in a Game Feature Plugin (/YourGameFeaturePluginName/GameplayCues), to the Gameplay Tag Manager so he knows about them!
Apparently when you initially add/readd them, somehow they get registered too, which is why it seems they are working, which in reality they are not… 
Some more elaboration:
Have a look at the custom GameFeature actions (especially GameFeatureAction_AddGameplayCuePath) as well as the custom LyraGameFeaturePolicy and the LyraGameplayCueManager of the Lyra sample project.
All of them have different functionality which I adapted to our game for handling gameplay cue tags in Game Features. (Bonus: You get a nice message when you add a cue tag that resides inside a non registered directory, hence reminding you to add the game feature action to your plugin 
)
I hope this helps someone else, and if any questions arise: I am happy to help! 
Greetings,
Markus
Bagpack Games