I am experiencing the same thing, a couple of things seem to work ... Close rubimine, delete the .idea folder ...
sudo rm -r .idea
(if macos or linux)
... and restart until they fix it
AND / OR
In Rubymine go to file> Open directory> go to the desired directory or file, this should update the view, do not add the .idea folder to git (if you use it)
Not great, but you can get around it
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