There is a thread by one of the beta users in the beta forum that expresses this matter. I found a workaround, and posted it there. It is:
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First, disable auto-import and have MC not fix broken links. This is important.
In a view, show all the files you want changed, including their particles and even artwork.
Select all the files, and in the tag action window, edit the Filename (path) field. Enter an expression that will change the path to your needs. For example:
=replace([filename (path)], \BackedUp\, \)
You might be tempted to manually change the name. Don't. Use an expression like that above to do the assignment; you're going to use it again so that conditional changes are made.
As soon as you hit enter, confirm you want MC to change the field (shown as Filename). MC will then get grumpy, complaining about a tagging error for the real files. Laugh at it, and click OK. You'll notice that the path to your particle files no longer match the path to the main file.
You can have MC remove the empty folders when it asks.
Now, here's the trick. Do the same thing again, with the same expression and you're all done. Since the expression above is semi-conditional (it can only change \BackedUp\ if it exists in the path), the fixup will complete the broken paths.
If the expression above is insufficient to ensure pass 2 will only hit the remaining files, it needs to be modified appropriately.
