I've been able to confirm that after a server restart from this plugin, all players join back, and are found dead, with all inventory gone. If I remove the plugin, manually restart the server. Everything is fine. If I remove the plugin and use a batch file (.bat) to run the restart (unscheduled), it still works fine. But as soon as we add this plugin back and mark the 2 times for restarts, it's doing it every time. Why is this happening?

Thanks!

This plugin does not interact with players in any way (besides kicking everyone just before the restart happens with the message), so the behaviour is indeed strange. Have you tried a clean server setup with just SmoothRestarter to see if it is still a thing?