I had this problem on my 4S. Original battery APN 616-0579. Bought a replacement battery APN 616-0580 (said was compatible, couldn't find a way to order a specific APN). Worked fine until I tried to upgrade the iOS version, then got persistent errors (error 29 on restore). Put back in old battery, and the iOS update went fine.
So every time I have to update iOS, I have to swap batteries, and then swap back. What a pain. I wish they would not claim multiple APN #s are compatible because they are not, they should have this info where they sell batteries and let you order a specific APN #.