I have a problem is that I have an item with the id ENDER_PEARL and when I go to the server and I do a right click it opens the menu I do with chestcommands and in addition it launches the ender pearl and send me to the targeted place and I would like that when I do a right click it does not launch the ender pearl

This should be what you are looking for;
https://github.com/RockinChaos/ItemJoin/wiki/Creating-Items#currently-available-itemflags

cancel-events - Prevents the player from opening a chest while this item is in hand or any open-able items. Useful for canceling the event of opening a book to set custom book items.

Set itemflags: cancel-events to your item to cancel the ender pearl launch event.

Let me know if this resolves your issue.

EDIT: After reading the cancel-events description it does look like I need to update it, haha. It essentially just cancels any events associated with the item itself.

Little confused by your question so I am going to interpret it as best as I can.

Inventory-Modify itemflag prevents players from moving the item.
itemflags: inventory-modify

or if you have it globally enabled in the config.yml

Prevent:
  itemMovement: true

If you are wanting to ALLOW movement simply set the config.yml setting to false and remove the inventory-modify itemflag from the items.

EDIT: Marking as inactive please re-open this issue if I did not answer your question.

Thank you

And also I have another problem is that I cannot do so that we cannot move the item in the inventory