...but now all of the markers have lost their references and we can't figure out how to re-link.
automatically referenced markers do not work across multiple files (so there is no fix for this unless you merge model and book files back to one file).
Reason:
an externally attached view (a drawing with a marker on it) placed on a layout in your book file cannot 'see' referenced view (drawing) as it is buried in your
model file structure. In order to keep this reference alive AC would have to open and regenerate model file (as the marker is placed in the model file) each time you move referenced drawing, which is not really a desirable solution.
so eg. a plan drawing with section marker 1/A250 (referring you to the layout A250) would be out of sinc if you moved the section 1 drawing to the layout A255 without opening the model file. The computational and network overhead (we are talking about big TW2 files right) to do so would be tremendous, not talking about dangerous situation if the sinc fails (temporarily out of network connection etc) and you would be left with inconstant documentation.
Does it make a sense?
::rk