Hugo Forss

Happens to me too.

OS: Mac OS X (ver 10.11.6, arch x86_64)
Java: 1.8.0_60 (by Oracle Corporation)
Launcher: Minecraft Launcher 1.6.61 (bootstrap 5)
Minecraft: 16w39a (updated Wed Sep 28 15:33:50 CEST 2016)

Just noticed this issue on Mac OS 10.11.4 when looking through the log after what I assume was an unrelated crash.

[11:03:00 INFO]: Minecraft Launcher 1.6.61 (through bootstrap 5) started on osx...
[11:03:00 INFO]: Current time is Jul 4, 2016 11:03:00 AM
[11:03:00 INFO]: System.getProperty('os.name') == 'Mac OS X'
[11:03:00 INFO]: System.getProperty('os.version') == '10.11.4'
[11:03:00 INFO]: System.getProperty('os.arch') == 'x86_64'
[11:03:00 INFO]: System.getProperty('java.version') == '1.8.0_60'
[11:03:00 INFO]: System.getProperty('java.vendor') == 'Oracle Corporation'
[11:03:00 INFO]: System.getProperty('sun.arch.data.model') == '64'

[...]

11:05:11 FATAL]: Fatal error launching game. Report this to http://bugs.mojang.com please!
java.io.FileNotFoundException: File '/Users/tasnu/Library/Application Support/minecraft/assets/indexes/legacy.json' does not exist
	at org.apache.commons.io.FileUtils.openInputStream(FileUtils.java:299) ~[launcher.jar:1.6.61]
	at org.apache.commons.io.FileUtils.readFileToString(FileUtils.java:1711) ~[launcher.jar:1.6.61]
	at net.minecraft.launcher.Launcher.cleanupOrphanedAssets(Launcher.java:254) ~[launcher.jar:1.6.61]
	at net.minecraft.launcher.Launcher.performCleanups(Launcher.java:496) ~[launcher.jar:1.6.61]
	at net.minecraft.launcher.game.MinecraftGameRunner.launchGame(MinecraftGameRunner.java:231) ~[launcher.jar:1.6.61]
	at com.mojang.launcher.game.runner.AbstractGameRunner.onDownloadJobFinished(AbstractGameRunner.java:186) [launcher.jar:1.6.61]
	at com.mojang.launcher.updater.download.DownloadJob.popAndDownload(DownloadJob.java:122) [launcher.jar:1.6.61]
	at com.mojang.launcher.updater.download.DownloadJob.access$000(DownloadJob.java:12) [launcher.jar:1.6.61]
	at com.mojang.launcher.updater.download.DownloadJob$1.run(DownloadJob.java:86) [launcher.jar:1.6.61]
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) [?:1.8.0_60]
	at java.util.concurrent.FutureTask.run(FutureTask.java:266) [?:1.8.0_60]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [?:1.8.0_60]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [?:1.8.0_60]
	at java.lang.Thread.run(Thread.java:745) [?:1.8.0_60]

It seems unloading the chunk is enough, plus it only affects newly placed stairs. I was working on extending a staircase I had built previously and then went away for a bit. When I came back all the new steps had disappeared but the old ones were still there. Lighting isn't updated so one can still tell where the stairs were placed.