Created a dedicated server on 7/12, copied over my daughter's world files, and fired it up, and everything worked fine. Everyone had their inventory, full ender chests, etc. 

Yesterday, they couldn't log on because "server is outdated". She told me an update was release, so I downloaded the new version, copied it into it's own folder, copied server.properties and permissions.json, as well as world data, and restarted server.

When we logged in, we started at world spawn with no inventory. We got around this by loading the original world on another client, moving everying to chests, and recopying the world. While this mitigated the inventory and ender chest issue, all the pets (cats, dogs, and parrots) were unresponsive to sit/unsit commands. It was like they belonged to other players.