Have you tried ssh'ing via ec2-user and running ls -al /path/to/folder/with/files/rstudio/is/not/showing?
This will list the permissions of your files and who can view it. https://chmodcommand.com/ is a useful learning tool. If you are not familiar with chmod, chown, and Linux user groups it would be useful to research these. (I'm making a presumption here as part of the troubleshooting process, so apologies if you are already fully familiar with everything I've mentioned?)
Could you ssh in as ec2-user, switch to your rstudio user (su - rstudio) and try to list your files? I'm presuming that you won't be able to list them as your user won't have permission. If that's the case you'll want to change your permissions and/or ownership (ie. chmod and/or chown {or maybe even create a user group for all your Rstudio Server users and apply that})