I've been gradually getting some answers over on the 3DS hacks reddit, but thought I would spread the burden out here as well.
The short version of my problem. I have a legitimate copy of PixelMaker Studio on an NA New 3DS. I would like to transfer it over to my JP New 3DS LL. However, the .cia created via gm9 fails its first-time extdata setup (acts as if there is no SD card inserted) when installed on the JP device. It seems like the .cia has some remaining console-tag information that lingers, which causes it to not find its target directory when installed on a new device. Unfortunately this prevents the software from proceeding into a usable state.
I can confirm 100% that it is not an SD corruption issue. This .cia installs, runs, and successfully sets up initial data on either SD I have when formatted and used on the original NA device.
I have tried creating a .cia from a fresh install that has yet to do the first-time SD card setup in case there was some flag that got thrown, but the same issue occurs.
Checkpoint does not see any extdata when the .cia is installed on the JP LL device.
So, my question is: is there any other method for creating a .cia that may be able to remove this tie it seems to have with the original NA device? I have used the gm9 'standard' .cia creation method.
OR, is there a way for me to inject backed up extdata for a title PRIOR to it creating that data itself?
Thanks in advance for your time and help with those two questions.