Why only 2/3 of the blockchain data can be pruned?
Think about it like this: If you pruned 100% you would have nothing, your node, and wallet connected to your node, wouldn't be able to do anything. So how much do we actually need to keep to still be usable? Well, once we've verified every transaction, we no longer need the signatures, so they can be ...
Ended up deleting the whole blockchain (94GB) and resynching with the --prune-blockchain start up flag for Daemon set in the miners wallet gui. This took over 5 days but I now have a 29GB blockchain a saving of 65GB!
Simply explained from jtgrassie's answer, you download the blockchain first, then prune it.
This is now done automatically. When you run a node, it will be pruned and you don't have to do anything else.