What I've done so far, I ran a read+write test with h2testw and it found no issues. Chkdsk also found no problems. For fragmentation concerns I moved everything off the card and then back on. I also checked my ZTD and MOF cias with godmode9 and they reported success. I did not however, reinstall those titles. Also as a mention ZTD was installed a month ago whereas I had MOF for much longer. With just these tests in place, the issue remains. Also, about the "show NAND or user string in system settings", what am I supposed to do with that? Yes I can see the change in string when I activate the option, but what else? I am running Luma 9.1 and also AFAIK GM9 refuses to launch a .firm if its hash doesn't check out. I launched Luma from GM9 and it worked.
Installing fresh copies of the games on a separate SD card was to isolate the problem between your SD card and 3DS firmware.
Also, reinstalling the games that are already on your main SD card would have erased your saves.
You can try backing up your
ticket.db in GodMode9, restoring to an earlier SysNAND *.bin image or use CTRTransfer, update to 11.9E through Recovery Mode or System Settings, and then restoring the lost tickets by reinjecting
ticket.db or using
faketik.
This is if you're absolutely certain those two games are clean installs coupled with good SD card and up-to-date custom firmware.
You should back up all the saves + extdata with Checkpoint or JKSM before doing anything else.
Edit - For GBA VC, saves are handled with GodMode9:
For DSiWare, you can back up the
twln.bin found in
[S:] SYSNAND VIRTUAL.
...
I am running Luma 9.1 and also AFAIK GM9 refuses to launch a .firm if its hash doesn't check out. I launched Luma from GM9 and it worked so a corrupt CFW firm file isn't at fault either. I have not yet tried to reformat 64KB down to 32KB cluster size to see what happens. So far all homebrew I ran(mgba,snes9x,duke3d,nestopia.....) never had issues.
I'd also like to add that my partition alignment checks out(had this initially formatted with SDformat for partition alignment - which forced exFAT, then I reformatted that partition - without any resize - to FAT32 with easeUS).
I caught your edits late.
Hmm, Another thing we can try is you provide your decrypted saves for the two games. I region change my n3DSXL with 11.5 EUR n3DS CTRTransfer updated to 11.9E. Install EUR copies of ZTD and C:MoF, restore the saves, and see if I experience the same problems with HBL black screen.
I may need to ask what your CRC-32 or SHA-256 hashes are for those games dumped in GM9.