I used to use menuhax before i installed A9LH a while back. I vaguely remember that there's a file on your SD card's root. Something called "boot.3dsx" or something like that. It sounds like you put the homebrewlauncher boot.3dsx in there thereby overwriting the ctrbootmanager boot file. If you show me a pic of your SD card root i'l be able to tell you more i'm sure. Or maybe someone who remembers better will come along to assist you.