Minecraft clickable held item

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.

Minecraft uses the "edge" of an image when creating the 3D geometry. That means the pixel that defines the "edge" will be used for the full color.

In your case, the edge of the sword is of varying color and alpha values. This makes the sword picture "smooth" but it will mess up the color picking used for the 3D weapon. I would advise re-working the edge of the sword to fix the transparency. A hard edge is going to work best.