I may have found the issue. The last four citations I imported either from DOI, CrossRef, or PubMed imported just as @misc{nameyear}. I tried knitting the document and got the error
(line 661, column 1):
unexpected "}"
expecting space or ","
Error: pandoc document conversion failed with error 4
I went in and removed those four citations and restarted R and the citation functionality was restored. I say that I may have found it, because I added the potentially offending citations back to the references.bib file, tried to knit, failed to knit, and then tried manually inserting citations and the citation functionality was still working. I can't identify anything else I did during this process that would have fixed the issue, or what I did to break it in the first place.