After returning from the nether, entities such as beds and chests where invisible until used, and the contents of chests and patterns on banners were reset.

Steps to Reproduce:
I have tried but failed to reproduce this, though my tests were on brand new worlds with very few chests and very few explored chunks.  It originally occurred after accidentally throwing an enchanted item through the portal, though this could have been unrelated.  I hope this can point you in the direction of an issue.