I have now several students reporting the same issue that I mentioned originally in the post Possible to recover lost Rmd file?
The students edit a rmd file provided in the assignment project, save it, and try to knit to pdf.
The resulting pdf shows none of their work, only the original file form the assignment. When I look at their Rmd file, I can see some of the chunk outputs in there, but the actual code chunks are gone! I can see in the Console and in the History tab that the code was originally executed when they interacted with the Rmd file in the editor, but it must have been removed in the knitting process. This seemed to have happened to 3 out of 19 students that worked on this assignment. The project in which it happened last is
You can still see the opened Rmd file with the chunk outputs but no chunks in there.