There is a way around this however, but you'll need a hex editor (I use HxD as it's free -- get it here: https://mh-nexus.de/en/downloads.php?product=HxD )
So, we need to find a decrypted .cia and extract it's contents before we begin. See my previous tutorial for information on how to do that (viewtopic.php?f=80&t=45583)
1. Open DecryptedExHeader.bin with your Hex editor.

2. Locate 3 addresses that are 3 bytes long:
0x1C9
0x201
0x230

IMPORTANT NOTE:
In my example, the ID of my game is 02 F4 03. When you change the number it MUST BE IN THE FOLLOWING FORMAT:
XX XX 0X ------------------> That ZERO in the last byte is very important
For instance, your Unique ID could be FF FF 0F, but it COULD NOT be FF FF FF.
The second to last digit MUST be zero!
3. So, once you've finished editing your id, save the changes you've made in the hex editor then run 3dsbuilder to compile the .3ds
4. Optional: use simple cia converter your newly made .3ds into .cia and install it to your 3ds!
Good luck!
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