Thanks for all your comments. After many hours of removing/reinstalling R, R Studio, tinytex, Miktex (and removing Miktex again), every library I had, and then sequentially adding my .rmd code until it broke, I discovered an offending extra ] in an R chunk far away from where the errors were being reported, things settled back down to where I was before the problem began. My guess is that the extra ] was wreaking havoc with the chunk options in the next chunk that caused the cropping of the figures. Now, both of the issues (couldn't compile with two out of 12 chapter .rmd files but could if I removed them plus the figure cropping) seem to have resolved. I've been using both rmarkdown, bookdown, and beamer since their inception, and it just goes to show that complacency is never a good attitude to have. Thanks again.