I'm well aware that this might be crazy and totally wrong - but I set off two long running r processes on RStudio Server, from two different logins, from two different machines (both processes were running on the same server).
It's a long loop that saves a file every iteration, so I'm able to see by the time stamps on the files if the process stopped or paused.
Of my two processes, one stopped on Friday afternoon (after my machine went to sleep) and the other continued to run all weekend. When I logged in this morning the process that paused started back up with no issues or errors. I didn't have to restart the loop or anything. I actually thought it had run all weekend until I looked at the timestamps on the files.
One difference between the two scripts was that one was popped out in it's own browser window and the other wasn't. The one that paused was the one that was popped out. Could having a script popped out trick RStudio server into thinking it's been inactive for more than 2 hours and cause it to timeout?