I have only tested this on a server I play (Vanilla with plugins) but when I leave my home and return my chests are invisible. They are trapped chests and ender chests (unable to test chests on that server). They stay invisible after a re-log/but are fixed when using version 1.10. I can fix the chests by opening them, then placing a block next to them, but they go invisible again after leaving the area. The chests hitboxes are still visible, and the ender chest particles are present.

Confirmed this is the server's problem, sorry I should have tested this more carefully first.