I haven't used the auto-save on either versions of SAI, but I can relate to the saving of multiple versions of a file. Every now and then the file will corrupt; I have lost hours of work before. Now I save like my life depends on it and I backup my files on either Google Drive or my backup HDD.

Possible helpful tip, if a file becomes corrupt while you are working on it. Don't exit out of the program right away. Usually it is just one layer that has an issue, which you can delete if you find it. You can find it by trying to paint or modify that layer; if you do so, an error message will pop up. You can still save everything else, however, even though you won't be able to save that layer. I do so by transferring all the other layers over (copy paste) onto an older version of the file. So yeah, you may lose that layer, but you can save everything else. Which is why I usually have multiple copies of the same layer while I work, especially if I am making major changes to the layer.

Pardon my long winded comment. Happy arting!

May be a helpful tip for others, thanks! Isn't relevant to the issues I was having (not a corrupted layer but rather a computer issue, I could get it to work making it compatible with windows 98 but then the program was super laggy), I've never experienced your kind of issue or ever really had issues with Sai saving at all before. I've been getting used to Sai 2 pretty good though, it has this *really cool* shape tool and I can select multiple layers and all this other mind blowing crazy nonsense. XD

Thank you!

I haven't used auto-save on either of these(tbh I don't recall even knowing they existed, i've used SAI 2 for over a year now), so this is nice to know, thanks!

You wouldn't have known they exist unless you look for it, there's like 2 versions hidden on the internet but I got my own made so I can customize my save time interval. I haven't looked but as far as I know there's no auto-save for Sai 2 that exists currently.
It also has a pop up letting you know if you're about to save as a not-sai/sai2 file which is nifty, like when you save a file as a jpg and continue working, if you forget you saved as a jpg you might continue saving your work in jpg format.

I've had same issue as you have, and lost hours worth of work when a file of mine corrupted and duplicate a save every two hours in case it happens again. I'm probably going to move away from using Sai when I find something else, although I find Sai so amazingly easy to work with. Shame I also don't submit my art on FA but maybe one day. I stick around for artists I really love seeing work from and you're one of them. Don't despair and you will make it better than you did the original. I've not had a file corrupt in awhile, and fingers crossed, I won't do as I never used autosave after that, and it didn't resurface. But I stupidly lost two pieces of art before I learned my lesson.