If by inject you mean "restoring" the file with checkpoint yeah. I tried the same with JKSM but still the same.
As a last resort here are the two unmodified save file of mine. The 3DS one is the dummy as you call it file with a playtime of only 8 minutes.
The CITRA one has playtime of 1 hour...
I'm facing the same problem. Trying to move the CITRA ACNL save file to my N3DS but I get a message that the save file is corrupted after importing it with checkpoint.
I did everything you said with the acnl-editor you provided but still the same even after changing the secure value.
Can you...