I did it!!!!!!
I know where the problem was. The problem is the redbutton Sky3DS when the gamelimit is broken.
The Sky3DS RED works like this:
0. Initialize Sectors of the ROMs (blinking first time when inserted new µSD)
1. Load game 1
2. Load save 1 while checking if ROM is registered. If not jump to 3
3. Load game 2
4. [...]
I have to break the sequence on no.2 before it changes the ROM so the ROM remains loaded. And here is the clue: In that sequence the Savefile is still written! If I break the sequence, the save is corrupt.
My workaround:
I have to load up 3 games.
The first two must be registered within the rom limit.
-The first ROM must have a working save.
-The 2nd ROM must have the gw-hacked save restored. This can only be done with a hex-editor, because DiskWriter checks for a valid savegame in the save-header.
-The 3rd ROM is Zelda also with the gw-hacked save restored.
1. I have to play the first ROM, so the EEPROM of the sky3ds is wiped and written with that save.
2. I exit the game and change the ROM to the 2nd Game. I don't load this game, because the save will be wiped if I start it.
3. Now I change the game to Zelda and break the sequence.
4. Gateway save loads!
This works, because Sky3DS don't wipes the save first, when it gets overwritten inside the EEPROM. Instead it is written sequencially. Maybe make a note in your start-thread that red-button sky3ds users can't use the save that easily