On upload your files are searched for localization and processed via that. You do not need to use the packager for localization anylonger. Due to this processing your hashs may change. The issue with the client is unrelated to this and being worked on as we speak :)
Could you provide an option to disable this? One of my projects is localized, but it has zero translations in it because it relies solely on Blizzard's global strings. I don't foresee myself updating that particular project since I consider it feature complete, but I don't want you going around my files and changing them to your liking. If you could scan files without changing them, that would be great.