Agree, this isn't a duplicate issue. The problem doesn't match the description of MC-138938.
Confirmed for 16w39c
Same issue - running server. I also have a guardian XP farm that uses the nether to bypass the mob cap. Mobs despawn when changing dimensions.
Also, if it matters... yes the first picture with the white/green texture problem is using a texture pack, but the same problem happens without the texture pack. Forgot to take a screenshot with the texture pack removed but it looks identical other than the GUI.
Sure thing; for 18W46a, fresh single player world (not upgraded from previous version) -
Fill shulker box with some assortment of items (doesn't matter if it's named or dyed) & place in the world
Log out
Log back in
Shulker box inventory is deleted, and any named shulker boxes lose their names
Notes: shulker boxes in player inventory or in chests retain their inventories; this only affects shulker boxes placed in the world
Chests, trapped chests, ender chests are unaffected