Red light means Luma3DS is corrupted in both your sd card and internal memory.
Replace the (Luma3DS) Boot.firm file, and set up Luma3DS ctrnand like it shows here and try again.
Do you see an error when you try to boot into Luma3DS?
It's not about it being up to date, it's about running it even if it's up to date in hopes of replacing any corrupted system or fw files, if that's what's causing the problem..
Missing installed titles from the home menu means your tickets are missing, sd card related problems, or the Nintendo 3DS folder is not present..
I'm taking your word for it that your sd card was properly tested with h2testw, while it was completely empty, and with the read & write setting. And was formatted before and after the test as Fat32 32kb clusters..
Also, does it boot into the home menu when the sd card is not inserted into the system? Or just the same?