Thank you for the fast reply. I'm aware of Boop and it is Windows only. Emulation via Wine used to work (kind of), but isn't anymore. Don't ask me why. The QR scanner only works with valid URLs. So I assume the file in question has to be somewhere online? Or is there a way to stream the CIAs directly from your computer?
I'm also familiar with FTPD and use it every now and then in conjunction with FileZilla. Although this appears to be the most reliable way to put stuff on a 2DS/3DS, it is also the most complicated and time-consuming. I always try to avoid it especially for larger files.
Why did the script stop working anyway? Was it due to changes in later FBI versions? If so, is there an older version of FBI somewhere which is still compatible?
I'm not too knowledgeable about the actual specific infrastructure with 3DS, but it's probably fair to say that it's merely obsolescence. This program ceased to receive updates, however, it's dependencies likely continued to be updated well past that point, meaning that it probably doesn't know how to interact with these updated dependencies, be it them changing how they do things or how they're structured. This is especially possible if only because with the death of the 3DS announced, I've noticed the modders who still fiddle with the 3DS have grown far more emboldened as we don't need to worry about future official updates breaking homebrew or figuring ways to circumvent new security measures. While hypothetically it'd probably be possible to still use this if you lined up the old versions (both 3DS and whatever CFW you're using) it'd be a lot of extra effort you would eventually have to undo to take advantage of updated or new Homebrew.
I agree FTPD is definitely the most complicated and, sadly, error-prone. However, in terms of system blindness PC-side, I can't rightly say I know one. Assuming you just want to install CIA games or some injections, the one thing I can suggest is the hShop. It's an archive of games that were on or are meant to be played on the 3DS. They recently released a QR code that installs a pseudo-eshop with direct access to that archive.
I am unaware of GBAtemps regulations on potential piracy vs. archival records, so I'll refrain from posting outright the link. However, you will find what I mean by looking up "hshop erista 3hs" in your search engine of choice.
EDIT: You are also correct in that the QR code is a link to a direct download. I simply assumed/hoped there may be one offered for what you were trying to get. Also, I do not know how to get earlier versions. Most of what I'm saying is based on conjecture and personal experience.
I'm sorry for not being of more help. I'm a bit foreign to Linux these days.