I've had the launcher "update" my modpacks a few times but it will backup the previous one in the .ftblauncher folder. On Linux it is in the home folder and I guess for Windows that's in AppData or something, same place as your regular .minecraft folder.
Still, I don't trust that backupping after I had it happen the first time. I did lose my customized configs and temper so now I backup the pack manually although I'm playing on a server now so haven't done that for that pack as there isn't much to save from a reinstall.