How are you bringing it up? You should definitely be able to just remap the root folder.
When I open MB, if I go straight to File > Library > Remap Music Folders the a dialog box pops up and lists every single folder in my root music folder (apparently requesting me to remap every single artist folder).
It's a confusing interface. Those are directories that have already been individually remapped. They're the same left and right, correct? The ones I originally did when I switched to MusicBee are still there in mine. Both sides show the correct mapping.
Those can be cleared out or left there (provided they are, indeed, the same on either side).
Just do a line of OLDDRIVE:\OLDBASEPATH -> NEWDRIVE:\NEWBASEPATH and run it and you should be fine.
I had worries at first that it was dynamically remapping all the time. But it's not. Once it's remapped it's remapped. You can verify by looking at the paths listed for a few of the files after the remap.
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