Have a workaround for this
1. have the game + the last update and/or dlc
2. start a new game to generate a new save file
3. immediately save your game (the save file should be 3161ko)
4. stop the game
5. apply the latest update (2.0.1) and/or dlc
6. start the game with the same save file you created
7. make a MANUAL save
8. stop your game again
9. check your save file directory (should be 4300ko)
10. launch PKHeX and select your save file and you should be good