I did search and found resolved issues for 18w44a. Since this wasn't an issue in 18w45a I am starting an new ticket. 

Made shulkers in 18w45a, couldn't dye them because of the issue with dye, so I named them. 

Copied world from 18w45a to 18w46a server. Started new server, logged in. Went to my tree farm area where I had two shulker boxes. Both named and had inventories in 18w45a to find that on the 18w46a server their inventories are gone and they have lost their names.  I did not log into the server in the same chunk as the shulker boxes. I checked all my other chests/enderchest and they seem to be fine. 

I went to make sure in the old server there wasn't an issue. Started up the 18w45a server that I copied the world from. I went right to the shulker boxes and didn't have any issues in reading the names or interacting with the inventory.