Answer
Check the order of your cache-clearing steps — refresh the Dictionary cache from IEE first, and only after that's done, log into Aurena and clear its projection cache and metadata cache via their respective cache-clear URLs. Clearing the Aurena-side caches before the IEE Dictionary cache has been refreshed can leave the Custom Action still missing from Page Designer's Command list even though every cache has technically been 'cleared' at some point — the sequence matters, not just whether each step was performed.