I am assuming you are not storing the entire blockchain now that we have DB,but maybe that is incorrect?
Almost all NXT functions only need the most recent 1440 blocks, so if each machine kept those 1440 blocks locally, they can purge them after that. blockchain FIFO.
If checkpoint files are a bad idea, I can live with that. Is blockchain FIFO a bad idea too?
Of course I store the whole blockchain, this is what the db contains.
You seem to be talking about blockchain trimming or pruning. This is in the plans, but not that soon.
Downloading the whole db will take longer than just the blockchain.