Hekate should be 2 files, 'helate_ipl.ini' and 'patches.ini' in the bootloader folder.
I would suggest to also install the Atmosphere sigpatches because you wouldn't be the first person injecting the fusee primary bootloader from Atmosphere instead of the Hekate payload.
Can't find any threads about this particular issue on GBAtemp or the wider intarwebz. Saw one video on YouTube that seemed relevant, but it was some dude with the same issue, no solutions offered in the comments. :/