F3+A should reload all chunks to avoid having to reload the world, correct? Then it should "fix" for example MC-5694 or other visual errors. But it doesn't. Only closing and re-opening a world fixes it. F3+A was originally planned to prevent having to do that, so it's not working as intended.
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No, but I know what you mean. F3+A actually triggers the function (it makes all chunks blink once), but then they are still as they were before, the visual errors still remain until I re-open the world.

I believe when you reload them it doesn't change the information in the world, just refreshes it for you. So the problem isn't f3+a, it's the info in the world. Why I think this is since f3+a is usable in multiplayer, it can't be directly affecting the world information itself as that's controlled by the server, so it should only be refreshing the information from it for you.

But server-side the insta-mined block is still there (for some reason, but that may be harder to fix). So the client should tell the server, no matter of local or real server: Hey, I don't have any chunk information, please send them to me. And then it should have the exact same information about the chunks that the server has. But it's not the case in the mentioned MC-5694 or other cases where client and server have different "opinions" about chunks. I didn't test it with ghost blocks explicitly, but I guess it's the same there.

I've just tested it with ghost blocks and it also doesn't fix that. I assumed there that F3+A didn't change from 1.8 to 1.9, because somehow the ghost block machine didn't work in 1.9. Which is a good thing, obviously.

I agree: f3+a would be expected to act as a workaround for ghost blocks as well as ghost chunk errors.
Why it helps one and not the other... perhaps the ghost blocks are weirder than expected?
But - still not revealing ghost blocks as of 1.9pre4.

F3+A only re-renders the chunks (reloads the graphics). Thus, the bug is that F3+A does not re-request the data from the server, contrary to what was implied by what we were told that it reloads chunks.

Grum, if it works as intended, then please make it possible to really reload chunks. Logging off and on again can take quite some time on a weak computer and it's not fun. Pressing F3+whatever shortly and continue playing is way better. So if this is really not what F3+A is intended for, then I'll at least make it a feature suggestion at the Minecraft forum. Anyone against it?

@unknown, it's better to use Reddit
Did you try FN+F3+A?