On the CD Projekt Red Forums, Community Lead Marcin Momot revealed that save files from The Witcher 3: Wild Hunt on PlayStation 4 and Xbox One wont be compatible with the Game of the Year Edition when it releases on August 30:
"The save files on consoles wont be compatible between different game versions (GOTY vs regular version) as they are treated by systems as separate products. This is something thats not up to us. Sorry."
Momot also confirmed that a new Witcher 3 patch is coming, but it wont be out before August 23. Expect a full changelog on this update closer to August 30.
Answering some questions on Twitter, Momot said everything will be on-disc in the Game of the Year Edition, the Game of the Year Edition will have a separate Trophy/Achievement list, and the Game of the Year Edition wont have any additional content over buying the base game and Expansion Pass.
http://www.playstationlifestyle.net/2016/08/15/the-witcher-3-game-of-the-year-edition-save-files/