I didn't update the template or have even installed it, so you are best off asking CJ for what changes he's made in the update. But, if you uploaded the new template on top of the old one, then those files were still there because there was nothing to overwrite them with (I presume - If I've got you right).
But, the way that the template system works, is that you don't actually need every template file - For example, with the Fire 'n' Ice template, you only need the .html file, CSS file and images directory and in Template Configuration select the default template files for the rest (I think) - Have a read of this - it is for an older version of YaBB but is still the same concept (apart from the .cfg file) and I'm pretty sure there must be plenty of documentation in the YaBB Codex.
http://www.boardmod.org/yabb2/YaBB.pl?num=1105417484Sorry if that was a bit of a quick explanation, but as I've just said to my good friend Batchman, if I don't start to spend a little time with my 'real family' as opposed to my 'YaBB family' over Christmas, then I will literally be killed...
Have a play about with things anyway. It's worth installing a test board to test things on... It's fun, and should be fun... So, have a good look around and a good experiment, and most importantly, enjoy it, and enjoy YaBB.