Help with saves on checkpoint 3DS

I suppose that is something related with the secure value associated to the savegame

 

Perharps this can help you (if you want/need, read the entire thread)

 

I'm not sure this has anything to do with the secure value. For starters, Checkpoint automatically takes care of that. And secondly, as that thread indicates, a secure value problem would end up with the game complaining that the data was corrupted.

Please clarify: when you say "nothing changes", does that mean the game keeps re-loading your old save? Or does the game complain that the data is corrupted?

Also, are you playing the game from a cartridge, or from your SD card?

If all else fails, editing Pokemon save data is completely trivial now.

 

Are you selecting the cart and using the inject savefile? Cause it seems something is missing from that process.

 

Before you go nuts looking for alternative solutions: can you open the save file you're trying to inject in pkhex on a PC, and verify that your Shiny Lugia is there? You don't have to change anything – but if you've been trying to inject old save data this whole time, then that would certainly explain the problem.

 

I'm confused. Do you have a data file that shows you have Shiny Lugia in pkhex, or not?

 

Well, work through the possibilities, if you haven't already.
-Backup whatever save is currently on the cart and verify with pkhex that it contains the data you expect.
-Catch a new pokemon in the game, backup the save, and verify with pkhex that the backup contains the correct, changed data.
-Restore the first backup you made to the cart and verify in the game that the pokemon you caught is no longer there.

If all of that works, then it seems to me the only likely possibility is that you're not selecting the correct save in Checkpoint when you restore it.