I had similar problem recently, and it seems @josh is correct on the theory that rstudio.cloud is close before all files are saved.
I am not sure was it pure luck or it is indeed a solution. I tried to delete the project (move to trash), and hoping that Rstudio Cloud can terminate any running tasks. After about 1 hour, I tried to recover the project from trash, and it now opens!
BTW, immediately after moving project to trash, the restore is not working, saying a 500 server error..