I have a book consisting of several documents. They have a default master set. When I use Adv F&R to do any kind of replacemean, I get a dialog with the message: /home/rgheck/FregesTheorem.lyx does not exist. Do you want to create a new document? That's the right master, but in the wrong directory: The files are actually three subdirectories down.
I can't seem to reproduce with a simple test case, though. Why might this happen? Richard