A potential solution will be to delete the players file from within the world folder. This will delete the inventory and all of the saved settings for the player thus removing the item. Inside of your server's files and folders you will find a world folder which contains another file that holds all of the individual player data files.
If this is a concern and the player doesn't want to lose the rest of their inventory or saved information, you can have someone new log in, pickup the item, then delete their player file.
Alternatively you can just reset the world if you don't mind doing so which can prevent future problems. If mods are every changed or updated it is recommended to start on a new world to prevent any issues such as this.