Thanks for your advice, Michael. My box.com account has unlimited storage, but the amount of files I can synced is limited by my OS (Win8.1) as I have to make do with the older Box sync client called Box Sync (instead of the newer Box Drive). Hence I thought about splitting the upload into batches. All encrypted files will end up in the same Box account after uploading. In this case, I should not run into the issue with damaged vault structure even if I have only one vault, right?
Yes I will try Cyberduck. Also found this thread today where you recommended Cyberduck 4 years ago 
. I wonder if CyberDuck will run into any performance issue for syncing 1TB files in one go or I should break my upload into batches too. Any thoughts on that?