Not much else to say.
Armour with all types of protection (eg: chestplate with fire prot 4, blast prot 4, proj prot 4 and plain prot 4) gets those enchantments removed when a player removes the armour piece from their body and updates it. I'm aware that this might just be a setting that I've got wrong, but I'm not sure how to fix it. Thanks for any help you can give.

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EssentialsX doesn't alter item enchantment except for when you spawn an item in or when you run /enchant. Are you sure you don't have another plugin installed interfering with it?

Might be another plugin, I just tested it on a server with only essentialsx and it seemed fine. Thought it was essentials at first because the items got fixed when I removed it. Sorry for wasting your time.

No worries!