"Flushing" old results only applies if you are folding offline, then connecting specifically to upload. If this applies to you, then just do that sometime within 24 hours after the changeover.
If you are online full-time, then no problemo! Just be sure that you have a file named "autoupdate.cfg" in your folding directory, the file containing only a "1", and you're set. When the change occurs, your system will "autoupdate".
For more details, read any of the various "readme" files associated with the DF website or in the files you downloaded.