Apotheosis has a module that has a chance to give items bonuses. When it happens to the items it will constantly remove them and be added back causing it to constantly flicker up and down.

Hmmm. I intended to prevent external modifications to them. The replacement items should not have any bonuses but since the items are removed repeatedly, it must keep reapplying the bonuses to them; is that correct? I could remove or add a toggle for this "feature" but I don't know which to do.

Yea, it seems to keep trying to add new ones. There doesn't seem to be a way to disable it in the other mod so, a toggle on your end might be best.