Notebook citations broken?

After updating to the latest version of R and RStudio, when I open rmd files for notebooks I had written previously and for which the .nb.html files still exist (so I know I'm not mis-remembering), citations no longer work. If I knit to html_document output, they work as expected.

Has anyone else experienced this? It puts a serious barrier to using R notebooks for my Biostatistics class.

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