Upgraded to Plex Media Server version 1.0.0.2261 last week and it seems to have deleted all of my Cloud Sync content. This happened to me once before when I changed the file system location of my Media content. Just a heads up for anyone else who might have a lot of Cloud Sync content.
Happened to me as well… it SUCKS!
Can you post your server logs for the timeframe when the media disappeared ?
It may be too late for the info to still be in the logs though
