An improper method of joining a LAN server can cause the world to be "read only" and not save any progress. This is not immediately apparent as all nearby loaded chunks are editable and seems normal. Only when all players leave an area and return will they realise that progress is not being saved.

Steps to reproduce:

1) Start singleplayer minecraft game
2) Open to LAN
3) Run a 2nd Minecraft window and log in with unregistered name
4) In 2nd MC window start the same singleplayer game (by accident)
5) Realise error and exit SP in 2nd MC window and join Multiplayer LAN server as I had originally intended

Because the world has been opened elsewhere is seems to be read only, although nearby loaded chunks appear fine until you wander off and chunk is unloaded. This was most notable in the Nether. Player inventory does save.

The reason for running the 2nd MC window was to have a dude standing by a zombie spawner, accumulating zombies for the players to kill and gain XP.

This is an unusual scenario that most people won't encounter, but for those foolish and unfortunate enough to accidentally start SP instead of join LAN it's annoying losing hours of progress.