This is driving me crazy.
When I work on R Notebooks in RStudio, it is common for half the outputs to simply disappear. I wish I could diagnose the problem but it happens on multiple computers (Mac) at random times, and I don't see it happening in real time because the affected chunks are usually off the screen at the time. I'm using fairly recent versions of RStudio (installed/updated in the past year).
Just now I added, worked on, and eventually deleted a code chunk half way through the notebook. Every output below the code chunk in the notebook had been deleted -- everything above it remained. I don't think I ran the chunk.
Right now the html file is 11MB with half the images missing; the Rmd file is currently 31kB.
Any ideas what could be causing this?