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Daniel, this is a know problem and is fixed in the beta version of the product now being tested. If you carefully work your way up the nested calculations you should be able to copy/paste them in without breaking. You just have to get the order right.
That was the first thing that occurred to me--however, the nesting is not very complex, only one "level". I tried copy+pasting the base fields and then the ones that use those in their calculation--I still get the error.
I have the same issue, and similarly I find that the order of operations doesn't matter.
The issue seems to disappear when I have refreshed my extracts in the current session, and then return if I close and open the file again.