This is the correct tooltip for this item, it reports I have 12 ender pearls that was absorbed by the staff:

This is incorrect handling: You mentioned something about this being a dedicated server issue and packet issue where the data about the item doesn't get sent unless its in the players' hand.

This is now fixed in 1.12 release. I am not going to fix in previous versions as it requires a forge change which isn't present in those and likely won't be.