As I said, I don't think you need to worry about recompiling framework-res.apk for your battery mod as SystemUI.apk on its own should be fine.
If you do want to recompile framework-res.apk for some reason and you're still getting this error, you can get around this problem. You need to remove all mention of the files in these folders from public.xml and then delete the folders. It's a bit of a pain but it'd work.
Unless you need those images, in which you're out of luck for now and you'll have to wait for an update to apktool.
Sent from my Xperia Z using XDA Premium
..Have you tried Tickle My Android yet?