At the end of the night my computer was force-restarted by Windows update and judging by Chops' reply that could have been the issue.
That's definitely the cause.
As you said, you tried doing it while WoW was running, which, assuming you didn't type "/console reloadui" before uploading, the data currently in the mod had no yet been written to the hard drive.
The official recommendation is to always close WoW before uploading to ensure all the data is dumped to the hard drive.
But as I recommended in my previous post, typing "/console reloadui" at random points throughout the night will help to avoid the problem of WoW or your OS crashing.
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It's all in the reflexes.