Are there figures that are unique to the workbooks, or are the figures that do appear reproductions of figures from the main text?
I know how to fix this in a LaTeX project, and I think with time I could do it in PreTeXt. But someone who is not busy with end of term and better at xsl (hi Rob) might be able to fix it first.
If I had a book written in LaTeX, and an accompanying workbook, also written in LaTeX, I would use the xr package to point all references in the workbook back to the main book.
There's no built in support for the xr package in PreTeXt (or any mechanism for external references that I'm aware of).
For LaTeX only I think it could work but it would be very hacky and you'd get lots of broken reference errors during conversion, and you'd need the LaTeX auxiliary file from the latex build for the main book while building the workbook (that is, the PDF from LaTeX part of the build).
For other formats I think it would require a lot of work because you would need something distinct from the usual xref. (E.g. in HTML you'd be linking to another document.)