Thank you for bringing this new information to our attention.
I think I'm wrong about the earlier statement about the missing trace signaling to the motherboard whether it's TN or IPS.
Maybe the n3DSXL upper IPS LCD you bought isn't genuine. It could be that yours was made by an aftermarket 3rd party manufacturer that doesn't 1-to-1 replicate the genuine IPS panels. The panel probably has 400x240 pixels where it's missing the other horizontal 400px needed for the parallax barrier's 3D effect.
New Theory: Missing trace ?= no parallax signal.
Yes, having those
HWCAL0.DAt HWCAL0.dat and
HWCAL1.DAt HWCAL1.dat files either missing or set to the wrong type of display panels will cause image problems.
I don't recommend doing this if you're not comfortable messing with the CTRNAND or don't know your way around using GodMode9, but as an experiment you can easily recreate this scenario where the ghosting and super stable 3D does not track correctly.
DO NOT PERFORM THE STEPS BELOW UNLESS YOU KNOW WHAT YOU'RE DOING.
- GodMode9 → [1:] SYSNAND CTRNAND/ro/sys → press (L)-shoulder button on both the
HWCAL0.DAt HWCAL0.dat and HWCAL1.DAt HWCAL1.dat to highlight them in yellow.
- For safety in case you somehow mess this up, make backup files by pressing (A) → Copy to 0:/gm9/out.
- Press (Y) to [CLIPBOARD] select the two (2) files. If selection mistake has occurred, press (SELECT) to reset.
- Back out once with the (B) button. Press (Y) → Move Path(s). This will relocate the
*.DAt *.dat files to 1:/ro directory.
- Perform the battery trick in order for the bad calibration settings to take effect.
- Boot to HOME Menu. Observe the horrendous image quality.
- Move the
*.DAt *.dat files back to the 1:/ro/sys directory. Perform the battery trick again.
May 05, 2020 Edit - Sorry for the mistake. The correct spelling for the extension is supposed to be
*.dat without the capitalization.