The heldFood variable in EntityTreeSquirrel does not store the item NBT data in the squirrels NBT data.

Reasoning: "They only eat it for a second or two, so if you're hopping off your world right after you give a squirrel an acorn, it doesn't really matter. The squirrel gains food from it the second you give it to them anyways."

Even if the squirrel only uses the information for a little bit it should still be stored so that the network sync can occur more affectively.