I'm writing a book in Rstudio using Bookdown. I had to take a break and suddenly none of my cross-references work in the pdf version of the document although they still work in HTML. Before, everything was okay, but now no bib or equation or figure references work. I looked for an explanation and it may be due to pandoc version. I don't know what to do 
Can anyone help me?
Sorry to here this.
Can you share more about the project ?
Or at least about your version ? It is possible that updates of tools (like R packages or system dependencies like Pandoc) can break project.
Tools like renv (GitHub - rstudio/renv: renv: Project environments for R.) help pin R environment to get same version of Package.
For Pandoc, if you think it can be the issue, you can try a different version that you think can work. This package call pandoc can help you test older pandoc.
Though, we update bookdown so that it does not break on pandoc updates.
Can you share rmarkdown::pandoc_version() ?
Also can you try an example document like GitHub - rstudio/bookdown-demo: A minimal book example using bookdown and add some content like your cross reference to see if this works or not for you.
If you manage to reproduce we can try to help fix this.
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