No, uninstalling shouldn't remove the config. Alternatively, if you can build a package (depends on what distro you're using) then you can simply install over the top.
If you're going from the old release version to the new one, there's a migration script that will ease the changes in config.
All that said, I'd take a backup anyway, just in case... remember to maintain permissions if you just copy .hts to somewhere else.
