Cloud 9 is reporting that it will be disabled on June 30, 2019. Is the recommendation to migrate now?
According to this post from Malan on reddit:
In fact, you're welcome to start using it now at (https://ide.cs50.io/). We'll provide instructions this summer on how to transfer files from the old CS50 IDE to the new (and improved!) CS50 IDE!
Our good friend @Blauelf added a post (also on reddit) with these instructions on how to backup the legacy IDE and restore to the new one.
In the IDE, you can select a directory (like for example your ~/workspace) in the file tree and choose to "download". It will pack the directory into a zip file and let you download that to your local hard disk.
Also, you can "upload local files" to the VM. So you could upload the zip file and unzip it on command line to restore your "backup".