I had this happen after returning from a nether portal about 6 chunks away. I noticed a lag spike upon entering the nether for the first time ("Running 3533ms or 70 ticks behind"). Affected an entire chunk (the one my house happened to perfectly fit into).
All chests and furnaces in that chunk lost their contents. All chests and a bed were invisible and remained invisible after reloads and interactions. The chests only reappeared after multiple F3+A reloads, I can't get the bed to become visible.
And an enchanting table in a neighboring chunk shows no book.
Also found 2 spawners in separate chunks with invisible empty chests
world backup from before upgrading to prerelease 3
world backup from just before attempting to repair it
The house is at -940 74 -372
most nearby monster spawners appear to be broken, showing no mob and invisible empty chests. some affected spawners:
-872 -8 -214
-784 -43 -334
-842 -40 -221
-723 -20 -257 this one's spawner is intact, but the chest is broken, they're in separate chunks
a nearby ancient city seems intact