I use both twich and minion to update my add-ons, the version listed in Minion under the classic tab as an update for carbonite is the retail version, thus destroying the installed classic version.

I did checked WoW Interface page of Carbonite Classic, latest version is for Classic: https://www.wowinterface.com/downloads/info25328-CarboniteClassicwithallmodules.html ... Are u downloading the right version?