Hi there,
I am sorry to hear you are having trouble with an RStudio cloud project. There is a known issue where if an R session insides a project, it can cause some data to appear to revert.
We're working on fixing this issue, however, in the meantime, there is an R package which might be able to recover these files for you: https://github.com/jmcphers/rsrecovr
tl;dr:
remotes::install_github("jmcphers/rsrecovr")
rsrecovr::recovr()
to restore all the files in your project.
Please let me know if this works for you. And I apologize for the inconvenience.
-Andy