Stephen Zeoli wrote:

If you do not have attachments, but only notes within each thought, you
might try experimenting with using the selection function and copying
"text outline with notes," and see if there is some way to make that
work. You wouldn't do it with the whole brain, but in smaller chunks.
Probably not really any better, but worth a little experimentation,
maybe.

I wonder if with that option CT's auto-link function could be used somehow to re-link the files automatically.