I just updated my cart to and I've been really testing the newer features. I've been making a lot of really deep, bass-y, drone stuff. Each time I get to a certain point things begin to happen to my GBA. First the battery light goes to red no matter how much charge there is in the battery, then the screen begins to flicker. This has been happening to me for a while, especially when I get into the real low bass.

Now with the new update I've been able to push it a little further with the extra clicks from the R channel and metallic sounds from the N channel. Now what is happening is the battery light and screen will do their thing but then I'll just press a button while programming and the Gameboy just resets itself and I've lost my work. This has happened to me twice now. First time it did this it was the L button, and just now it was the select button. I save often but still end up losing stuff.

My guess is I'm just pushing the Gameboy a little too far and it is resetting itself for some reason. I'm curious if I keep doing this consistently will I do any damage to my SP? Has this happened to anyone else?

Sounds like a defective Game Boy. I don't think software can cause such behaviour, but who knows.
If you can reproduce the issue, please send the corresponding bank with instructions how to provoke a crash.

I was going to say the same thing.  If you can upload the .NL2 file I'd be happy to test it out.

It very well could be the Gameboy. I have a Frankenstein SP that I cobbled together from three different ones. I will attempt to make a reproducible nl2 bank file. The thing is that it's been inconsistent with how it resets. It's hard to replicate but I'll see what I can figure out.

Maybe the best is to begin with a safe non Frankenstein GBA ?
I've got some which are really difficult to deal with, so maybe you only have a hardware issue...

That's what I've been doing. I have a few other GBAs around. So far it's just making the screen flicker to the beat of what I'm playing.