How? You've been lucky, that's it. Over a year without backups is asking for trouble. But again the biggest issue is that you guys are acting like consumers for a legit product. It's not a legit product. There are no guarantees, nowhere, and this community is nice enough to provide you with tons of hours of free work to help you get started.
There is no "mandatory" thing cause you're doing hacking, you're not outside of Nintendo careful hands, heck you're stealing from Nintendo. People are nice enough to tell you every single step of the way what you SHOULD do, but ultimately this is YOUR decision. If you're actually a dev then it's really concerning that you would decide to skip these recommendations for such a long time.
Again if you're a dev, you're probably very aware that malicious people are everywhere on the internet. If you (hopefully) take the time to protect your computer against such attacks, why wouldn't you be doing that for a console as well? How hard is it to understand that when you circumvent security to install unsigned stuff, there is no longer said "security" and any app will be able to do whatever the hell it wants?
You can scream all day and night that these people are atrocious, but none of your complains will ever hold any ground in any sort of court because you're doing something clearly identified as illegal in the first place. You didn't get burnt for homebrew, you got burnt for trying to pirate an unreleased game. It's not a nice feeling but owning the responsibility is the first step to healing.
I WISH GbaTemp would actually hold up to their own words and not condone piracy, as it is so clearly the case here. This mess wouldn't be happening with people who are there for homebrew. When you're not starving to the point of needing to pirate something that isn't even out yet, you have more time to think about the dangerous situations you put yourself in.