Hi, I found this topic while searching for a way to make the oothax work on my N3DSXL at 11.7. Since I have the same problem as ashudow, exactly the same: 1 not CW consolle (N3DSXL), 1 Cw consolle (O2DS) and no powersave. After few experiments I found a few things I want to share with you:
1) IT IS possible to make the oot3dhax installer work with the HBL application, but first you have to start ocarina of time, press L+down+select ingame to open luma menu, select miscellaneus options, select to make the HB start from that application, press 3 times bb close ocarina of time and restart it. The HBL will load and this time the installer will recognize the cardrige.
p.s.: even using installer my save didnt work properly but i think its something wrong with the installer itself.
2) you actually CAN modify the save with JK save manager, first of all do all in step one, if it doesn't work DON'T delete the oot save, find JKSM.cia, install it and run it. Do a save backup. Go and get the proper payload (otherapp) from
http://smealum.github.io/3ds/, it should be a 27 kb file. Connect the sd to the pc and check the save folder inside JKSV folder (you should find a folder with the game name, inside it one named with the data you created it with JKSM or the name of the save if you named it). Here you will find 3 files and one of them is actually payload.bin (the one used by oot3dhax installer and probably wrong). Take the payload you downloaded from the HB site, rename it payload.bin and put it in the save folder overwriting the old payload. Put back the SD in your device, start again JKSM app, and backup the save. Done, the save with the right payload.
Now that worked for me and I really hope it will help other ppl with this issue. Cya, and thanks for this topic, I found a solution thanks to it.