For anyone using the Sonic X Shadow Generations 100% save on Eden and having Shadow work but Sonic show no save data, here is the fix.
Eden seems to split the game into two internal title IDs:
01005EA01C0FC000
01005EA01C0FC001
At first, I only placed the save files under:
01005EA01C0FC000
Shadow loaded at 100%, but Sonic acted like a brand-new save. When launching Sonic, Eden shows its loading screen again because the game switches to the second internal program/title ID.
The fix was to also put the Sonic save file here:
01005EA01C0FC001/gene_NX
So the working setup should look like this:
01005EA01C0FC000/
├── game0/
│ └── gamedata
├── system/
│ └── systemdata
└── gene_NX
01005EA01C0FC001/
└── gene_NX
After putting gene_NX inside the 01005EA01C0FC001 folder, Sonic showed the 100% save correctly. Shadow also stayed at 100%.
If 01005EA01C0FC001 does not exist yet, open the game, go into Sonic, let it create a save, close Eden, then check the save folder again. Replace the new gene_NX with the 100% one.
Make a backup of both title ID folders once everything works.