If the flag "enderpearl" is set to "deny" then it should block enderpearls from teleporting players, but also acknowledge that op'd players bypass this. If it is not blocking enderpearl teleportation, think about any plugins you have for enderpearl teleportation, and check/disable them to see if that impacts anything. If that doesn't impact anything, it is most likely something to do with your worldguard version.
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