I have no idea rly! It's just that both cards are originally 128 GB, and they have a large difference of usable space, which makes no sense.
Because your old emuNAND was 12 GB, and that isn't the standard size. When you created the new emuNAND partition, you selected the default size. So that extra space is still taken up, but probably isn't usable because your actual emuNAND (that you restored) is still only 12 GB.
You should be okay to just do a full sector based clone from the old card to the new one, since they are the same size. That will preserve the 12 GB size of the emuNAND. You can use DiskGenius to do that, or Win32DiskImager. Some other applications like Minitool Partition Wizard (FREE version, NOT the trial, they are not the same thing, the trial isn't functional and just asks you to pay to do literally anything) might work but in my experience they will often just ask you to pay when you try to do a sector based clone. I know DiskGenius works. Win32DiskImager works too but isn't as user friendly and you will need 128 GB free space on your PC to create an image that you can restore onto the new SD.
Alternatively, when creating the emuNAND partition in Hekate, you are able to select a custom size, but this size has to match EXACTLY the size of the old emuNAND, if it's too small it won't fit, if it's too big the extra space will (probably) be wasted.
You can check data management to confirm whether the 12GB emuNAND is automatically resized to 29 GB, it's possible that Hekate did this automatically (I don't actually know), in which case, you haven't actually lost any space. You just have to move some games to "internal storage" (which is actually your emuNAND) to reclaim the additional space taken up by the emuNAND partition.