[T-Mobile Samsung Galaxy S II SGH-T989] RealPariah:
It seems to also be statistics generated by android that also get involved (hence increased battery life over several days after an initial flash) and its those this process helps address. You are totally correct in that the batteries chip is only read and not written to and I am not saying you adjust the battery chip itself that would be nuts.

I can say at one point per my post on it one of my ROMs (an old version of darkside evolution) would hang on restarts and shutdowns. One time when I forgot to physically pull the battery it was slowly drained past it's safe point. I ended up getting an error even in my charge screen and OS would state bad battery and shutdown on me. I had to wait a day or 2 of no phone letting it sit, then finally got charge screen and left it there for another day. I then had errors but could restart after pulling and reseating battery. This went on for a couple weeks while I made sure to do full charge cycles to make sure battery was back in good shape. Finally after I felt it was back to normal I ran through this process and bam since then (about a year now) no more battery error and forced shutdowns and phone works perfectly. So, doing this saves me from buying a new battery and saved my a$$ big time. Had I not wiped battery starts battery would work, but the error would still be present and at issue, and had I not exercised the battery and wiped before I would have had severely limited battery life. Not all users know this and hence why I built a guide for users who don't have the time or knowledge to address this and not do much for developers and advanced tech users such as yourself who don't need it.

Kinda like do you require a guide on how to flash a new ROM? Probably not but they are there for users who do, but do you post replies asking why they are there or why developers put certain steps in like fully wiping data on every flash even though that isn't required in all cases? Or do you realize those steps are there to ensure the least number of issues for users who don't know when or why they should wipe data on a flash and avoid the replies asking how and why issues happened, and so you skip those while others find them useful.

So, it does seem through programmatic issues and other not accounted for errors true battery issues can happen, and following this procedure can truly help. While thankfully most people don't have this extreme of an issue again this process can help even if the battery gets slightly off.

I understand Google wanting to not even try to admit to the slightest problem as think about it then users would be asking for free new batteries at the slightest hint of trouble even if a replacement is not warranted for their case, but then what does Google do mandate users send their phones in for verification before new battery, make carriers or manufacturers responsible for this? Then if that happens would carriers or manufacturers enjoy the time, trouble and added expense of this? Not likely, they may in that case be less likely to want to create android devices if they were forced to openly deal with an issue like this.

Not to mention with custom ROM work that developer may adjust, add, or remove code in their work in an odd way that causes this and since those who root usually flash a lot it just means they are more apt to see issues (not to mention this segment is really starting to grow in to noon technically advanced users who would not bother to study up and be aware of every issue that could happen due to using custom ROMs). So all in all it's safe to say we don't see any issue, and your warranty is void if we see your device is rooted when you attempt to submit it for repair/replacement.