yes it will
but you'll have some *.new files hanging around (in /etc for example) but those are quickly removed...
I install with my Slackware 9.0 cd's, install swaret, and then it begins:
Insert my cd with crucial updates (I don't feel like downloading everything twice or more...) so glibc and gcc and the likes get updated, and then I run an update against a slackware mirror (easily configured). I see what else I would like, and I am before the final updates already running slackware 9.1
and now I just keep up to date by running swaret with the current branch ...