As of April 2015, the One Drive sync engine on Windows 8.1 is sophisticated enough to recognise the files, and avoid all of the issues I feared in the question.
I clicked on the notification area icon, and clicked 'Resume synchronisation'.
Changing One Drive’s default location is easy and has many advantages.
You can free up space on your system drive, reduce read/write operations that cause wear on your SSDFor years, standard hard drives have been the speed limiting factor in overall system responsiveness.
I had to let go of some things, one of which was my comic collection.
Truth be told, it sat there as constant reminder of the comics I would never again touch because it was becoming too much work to organize.
It’s deeply integrated into Windows 8.1 and offers itself to become your one stop for Cloud storage and syncing across multiple devices.
As an O365 Home subscriber, I use my unlimited One Drive storage to store my files.
These include my pictures, videos, music and documents.
They are great for storing libraries, downloads, and Sky Drive files externally. To move it to another partition or an external drive, open the Windows File Explorer (there’s a shortuct in your Taskbar) and find One Drive in the left-hand menu.
Right-click it and select and pick your preferred location.