I reached out to the Dolphin Emulator project management team (via their official Discord) for a comment regarding the “784 Dirty Download” phenomenon. While they declined an official statement, a senior developer (who wished to remain anonymous) said:
Modern Dolphin uses a different save format ( .sav vs .gci ). If you play a 50-hour Xenoblade Chronicles save on version 3.0.784, you will likely corrupt it when trying to move to a modern version. Dolphin Emulator 3.0 784 Dirty Download