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I use LyX exclusively for note taking, rather than as document generation tool. I would have used emacs org-mode if it weren't for the fact that LyX allows me to enter math formulas and simple drawings in WYSIWYG mode.

I used to be able to insert cross references to a label in another file, and be able to click and have LyX jump to that label (as long as the second file is already open). Now after several LyX version updates, I can't seem to be able to do that. The label says "BROKEN: Ref: blah blah" and clicking on it just opens a dialog to edit the cross reference.

How do I make LyX behave the way it used to? I can't seem to find any good alternative to LyX for note taking with math formulas, drawings, and local storage (not web or cloud based).

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You need to have the child document inserted into the master document. Then you can use labels and reference from the child document in the master document. To do this, in your master document go to Insert > File > Child Document and select the document you wish to include.

If you don't want to actually include the child document because it messes up your PDF generation, you could try putting it in a note, this way you might still get access (within LyX) to cross-references from the child document.

Note that in the child document you can also use references from the master document.

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