Personally I wouldn't update, if later on, a fork that has been thoroughly tested is deemed a worthy replacement, a switch to use the fork instead would be fine. I don't think there is need to remove it completely from the repo if the changes do not apply to old versions.
This is merely my opinion, I don't really use Audacity, I've installed it in the past just to play around, the opinions of people who actually use it regularly should be given priority over mine.