I had several students report to me that the error happened when they were knitting the Rmd file to pdf. Their Rmd file now has some random outputs, with almost all of the code-chunks that produced the output completely gone. I have never seen anything like that before. I would not expect the Rmd file to get modified during the knitting process like this. I can see in the History tab that they did do bunch of work (I did not inspect it in details, so I do not know if the work was correct).
The rsrecovr package recovered nothing useful, it created two copies of the original Rmd file form the assignment, with my instructions but otherwise blank.
I will instruct my students to take a screenshot of the error if it happens again.