The battery patch containes 2 files.
build.prop (changes the wifi scan interval from 1.5mins to 2.5 mins)
and famework-res.apk, which contains changes supposed to help battery life (You'd have to do a file compare or ask Kejar for details if you want more info...)
Applying a theme will replace the framework-res.apk (which is why Kejar specifically advised NO THEMES during this test.. if you've applied ANY theme after you applied the patch, then you're not getting the benefits of the patch.
To stop using the patch, just install a theme, it will over-write the patch's framework-res, and you're set.
HTH!