After updating to the release candidate 9, I found some of the docs and files on my project have disappeared. My whole outline has vanished while other documents are still here. Anybody else have this problem?
Did you transfer/relocate the project file before opening it in 2.9.9.9? Or are you by chance storing your project on the cloud? Syncing issues are usually the culprit of missing work.
In any case, to recover your data you might want to check your backup files. You can open the backup folder from within Scrivener via File > Options > Backup. Click on the “Open backup folder…” button. Make sure to copy the zip files to a new location outside of the automatic backup folder before attempting to open them.
No, the update was fine for me, and likely for everyone else, or the forums we be flooded by now with posts similar to yours. 
I agree with the previous post. Check your zipped backups.
Best,
Jim
You can find L&L’s position on cloud usage here: scrivener.tenderapp.com/help/kb/cloud-syncing/.
Some of the articles are a few years old, but I assume that L&L has kept them current as needed (maybe a dangerous assumption).
The projects are not stored with the software. You yourself decided where to save each project when it was created. So updating or even deleting Scrivener has nothing to do with your project folders. You must have done something else to lose the project content.