Block Entities are not upgraded properly when upgrading from 1.12.2

I loaded my world in the new snapshot this morning which i have been playing in since the new 03 snapshot and it has been working fine.

• Chests, shulker boxes and ender chests are invisible
• Chests and shulker boxes are empty
• Hoppers don't work
• Beacons don't work
• Furnaces don't work

Possibly related to MC-125106.