Are you sure you don't have emunand files in the /sxos/Emunand folder of your SD card?Can I use this to copy a hidden SX OS Emunand to a hidden Hekate emuMMC? Normally this can be done in Hekate through the migrate functionality but for me the options there are all greyed out. SX OS does show that the Emunand is enabled however and it also works perfectly fine.
Edit: what is strange is that Emutool says the SX OS Emunand partition is disabled while it is in fact working.
Also check if the SD card drive you're selecting in Emutool is the correct drive.
Anyway, even if Emutool for some reason does not recognize the sx partition as active (which is quite bizarre, please check everything carefully), you can still proceed with the copy as per instructions.
The Sx partition activation info are only a few bytes in sector 1 of the SD card, which are not part of the real data of the emunand starting at sector 2.
Ciao.