Looks like the system will treat the GotY edition as separate.
When CD Projekt RED launch The Witcher 3: Game of the Year edition at the end of this month, it will not be compatible with existing save files for The Witcher 3– CD Projekt RED confirmed that the Game of the Year edition of the game and the standard edition of the game will both be treated as separate products by the system.
“The save files on consoles won’t be compatible between different game versions (GOTY vs regular version) as they are treated by systems as separate products. This is something that’s not up to us. Sorry,” CD Projekt RED’s Community Lead Marcin Momot revealed on the CD Projekt RED forums. This means that not only will save files be kept separate, but other things, such as Trophy Lists, will be separate too. He also confirmed that a substantial patch would be coming for The Witcher 3 by the end of this month.
The Witcher 3: Game of the Year edition will launch with the base game, and both expansions, as well as all updates released for the game, on disc on August 30.