Nope.
1. Got payload_stage2.bin compiling this: https://github.com/dark-samus/arm9loaderhax
2. Placed it at /a9lh/ and extracted safea9lhinstaller arm9loaderhax.bin to the root
3. START
4. Brick
I heard that someone bricked his Old 3DS by only updating stage2 too.
It's weird.