That will depend on the mod and which files get updated. There is a chance that a few files will get overwritten and you will need to redo those few files, but you probably will not need to do all of the files, unless you choose the full install. Which brings up another point, I think the one click update on DH (may) be a full install. I am not sure on that. If it is on PHPBB’s web site is a partial install, helps out greatly with mods.
Hope this helps,