They will stay there, each time you load up the launcher, it will check the master server for any updates. If there are any, it will download them. The files stay, they are updated when they need to be. If there is anything missing, it will be re-downloaded when you run the launcher.
Only the files that are updated will be downloaded through the launcher, instead of downloading the whole version like always. Pretty sure this was explained a bit more somewhere in the OP or one of Badspot's reply's.