There are two main ways to sync item capability data: Override Item#getNBTShareTag, as suggested in this PR and various other issues. Register an IContainerListener for EntityPlayer#inventoryContainer on PlayerLoggedInEvent and PlayerEvent.Clone and for PlayerContainerEvent#getContainer on PlayerContainerEvent.Open. I use the latter in my mod. This class is responsible for registering the IContainerListener instances with each Container, this is the base class for the IContainerListener implementations. The implementations are here, here, here and here.
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