This could explain it. But I would assume that a raw clone/image would copy over the MBR partition format as well. Maybe it depends on what program you're using.
It does, it leaves the USB Pendrive in the same state that the Wii U left it, in other words, it looks the same before formatting the device for the PC use.
The 64GB Pendrive has games on it, the RAW image copy has them and when I format my Pendrive in NTFS and *THEN* I restore it with the image file, the Pendrive recovers everything and the Wii U recognice it and uses it without problems. So, this works fine for backuping and using it with the same device. But, it defeats the purpouse of having a backup to use on other hard drive if the HDD fails (and my HDD is about 8 years old, so well, I'm just looking for some backup solution without having to buy another one for now).
I tried doing the same with my HDD, using the same Pendrive image, and it does not work. I mean, the image it's perfectly fine because it works with my pendrive without problems and the games boot and plays (BoTW works perfect). But not with the HDD, which it makes me think that the Wii U does have keys per-drive and stuff.
Also, note that when you have a HDD with a MRB partition for example, the Wii U will ask for formating, but using my HDD with the Pendrive image doesn't, the Wii U recognice the device and it doesn't prompt for formatting, but also it refuses to use the device and doesn't display the games on it, which in other words means that effectively the Wii U it's doing something to know that a device was cloned, in this case, cloned my Pendrive into my HDD. Ah, and I forgot, if you ask how I know the Wii U recognices my device even if it's formatted, it's because everytime I connect or disconnect my device the Wii U tells me to do it only when the console it's off.
did you try 2 flash drives of different size? Thats what i did because at the time i did not have the drives i do now. I used a 256 mb flash drive and an 2gb flash drive. Acronis is not free but if you know where to get it.......
To test the data i played That nano assault wii u eshop game as its entire size is under 100mb i think. game worked from the cloned data just fine.
Sadly, I don't own 2 64GB Pendrives, so nope. I used my 500GB HDD for that and my 64GB Pendrive, but I doubt it will change a thing if we consider that the Wii U stores the console keys and device keys.
The original device was the 256MB and it was cloned to the 2GB? Unless Acronis does some kind of process to modify the keys the Wii U makes to make it fit to the new device (which it's unlikely) then it's pretty weird that that worked. Being realistic, I doubt that using Acronix here will work, but since you did say it with confidence I'm really curious, so I will give the 30-day trial a shot and use that to see how it goes.
By the by, what version of Acronis are you using?
EDIT: Nah.... I tried using Acronis True Image Home 2019 and it wouldn't even recognice any drive that's formatted by the Wii U.
The only backuping solution that comes to my mind here it's using wfs-fuse, mounting the drive on Linux, and start copying files, but I think that the limitation to this is that the program can only read files, not write, so.... we are still stuck here.