That gpu choice hurts my heart, so much bang for buck missed. 750 ti are still on sell at most retailers still. Never hurts to be future proof (noticed you said you were in ps3 gen games) in the gpu area especially in gaming. You could of kept that i3 and opted for a newer tier for just a few...
Yes you installed it correctly , the same thing occurred last night on my n3ds on 11.2. I proceeded and updated to 11.3 as well and A9LH was intact. Good job man!
If you delete it , the console will not power on completely on next boot since the payload is missing, First it searches SD and if not found searches CTRNand for arm9loaderhax.bin. If both missing the system powers off.