It seems like your SD card may be broken. If you have something in /luma/payloads, try executing it (it should start with the bottom it name says). If it works, the your SD card is working fine and I won't know what's your problem.
Well I have the start_Hourglass9.bin, if I recall preperly I need to start or select during boot to run it?
But you may be right coz I did some manipulations on the SD including multiple partitions, but I deleted all partitions using a partitioning tool.
Is there anyway I can fix it or at least check if it fine?
So in theory if I just copy all my old files in a Fat32 SD card and put it in my 3DS it should work?
To be honest I did this before with 2DS and it worked fine. But this is the first time I try it with the New 3DS XL.
Thanks.