We have large project with lots of packages. Sinse last week i found strange behaviour with some dialogues and zones: some of them available just in editor mode and do not available in runtime. I was check for object duplicates in packages but do not find something strange - all object contains just in one package. I've already spent a few days searching for solutions and so far the only option is to upload all the data in one package. It is not terribly convenient and breaks all localization in the game.
Also its seems to be working just in case that all dialogues and locations with zones located on one package. And i think the problem of this situation is reference resolving duting package load.
For example you have package A which contains reference to package B. If A would be loaded before B all these references would be broken. Also, if you try to avoid this bahaviour with export config (reorder package) this would be ignored during export and all packages would be order in order of it was created.
p.s. I sent a link to export the project and all the data in a private message to Nico.