If you did file operations inside a shell or for example using Nautilus Show archive.org snapshot , it can take quite a while until RubyMine takes note of them and updates things like your project tree or its internal file list.

Rails Long Term Support

Rails LTS provides security patches for old versions of Ruby on Rails (2.3, 3.2, 4.2 and 5.2)

• Prevents you from data breaches and liability risks
• Upgrade at your own pace
• Works with modern Rubies

Read more Show archive.org snapshot

Flushing file system buffers Show archive.org snapshot helps you out (run it from a terminal):
sync

This is also possibly via the RubyMine menus: File → Synchronize.