In case anyone finds themselves struggling with water in a similar fashion; I reached out to Tyron directly and I got the following reply:
you can use world edit "/we ms" and "/we me" to select an area and "/we deletewater" to remove water inside the selection
In other words, use the magic wand/select tool to mark an area in creative mode, and then use the /we deletewater command. It works.
I can't believe it was that simple...
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Khornet's post in Removing water from a shared block? was marked as the answer