[Linux Mint] Error 05: You don't have 1 ID1 in your Nintendo 3DS folder, you have 0!

[LuineGR]

Hi there. I'm using Linux Mint 22 "Wilma", Linux kernel version 5.15.0-119-generic. Python3 version is 3.10.12.
Yes, I have UTF8 enabled.
I have an Old 3DS XL with version 1.17.
Python script logs are as follows:

MSET9 v2.0 SETUP by zoogie, Aven, DannyAAM and thepikachugamer
What is your console model and version?
Old 3DS has two shoulder buttons (L and R)
New 3DS has four shoulder buttons (L, R, ZL, ZR)

-- Please type in a number then hit return --

Enter one of these four numbers!
Enter 1 for: Old 3DS/2DS, 11.8.0 to 11.17.0
Enter 2 for: New 3DS/2DS, 11.8.0 to 11.17.0
Enter 3 for: Old 3DS/2DS, 11.4.0 to 11.7.0
Enter 4 for: New 3DS/2DS, 11.4.0 to 11.7.0

1
[--] Checking if SD card is writeable...
[OK] SD card is writeable!
[--] Ensuring extracted files exist...
[OK] boot9strap.firm looks good!
[OK] boot.firm looks good!
[OK] boot.3dsx looks good!
[OK] b9 looks good!
[OK] SafeB9S.bin looks good!
[--] Detected ID0: 429ec663ef049e1683557d90c54e9cca
[--] Checking databases...
[OK] title.db looks good!
[OK] import.db looks good!
[--] Checking for HOME Menu extdata...
[--] Checking for Mii Maker extdata...
[--] Found file in ID0 folder? 'b2a0014b47606ccb5344313600275048_user-id1'
[XX] Error 05: You don't have 1 ID1 in your Nintendo 3DS folder, you have 0!
[--] Consult: https://3ds.hacks.guide/troubleshooting#installing-boot9strap-mset9 for help!
[--] Press Enter to exit...
`

I followed all listed steps in the guide, but my user data was not temporarily wiped. The Settings app still recognised that the data was "corrupt" and reset, but everything is exactly the same as it was before (even my Miis were still there as they always are, but for some reason the Mii Maker still created extra data for the SD card).

[LuineGR]

Quick addendum: the troubleshooting guide only has instructions to deal with a non-zero number of ID1s, which leads me to believe that my situation is somewhat uncommon. I would've otherwise referred to it.