I have issues with Items not being destroyed when the base decays below them. They are all just floating in the air. Does anyone know a setting I need to change or if there is any solution to this? 



Thanks,

this issue is not related to TruePVE. TruePVE does not handle decay damage, nor does it prevent destruction of entities when their ground is missing

if this is a player's base that has decayed then your issue is another plugin is preventing storage containers from being destroyed when their foundation or floor is destroyed. you can search your plugins for OnEntityGroundMissing. if you find this then look for the word StorageContainer. if you see both together followed by return true; or return false; then that is your culprit.

if this is for raidable bases then you must disable the config setting Boxes Are Invulnerable

Which config setting? I don't have any other plugins that handle damage, I also seached everything and found nothing. Could it be to do with Aurthoirzed damage flags? or something that limits the item to only being damaged by a certain person?

What do you mean which config setting? The one I told you ...

Again, TruePVE does not handle decay damage