After 8 months using Smooth Restarter without any problem, last night I updated the version to 2.0.0 and this morning, at the time of the scheduled restart (06H00) the server started with all the default setup (vanilla map, without plugins, no map state or players, etc.)
What could have happened?

Plugin does nothing but restarts your server on demand. The issue you are talking about have absolutely no relation to the plugin itself.