If a sign is placed in a particular region and then a /clone or /fill command replaces the block containing the sign, subsequently placing a sign in the same location results in the sign input box being prepopulated with the text from the old sign.
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Is there any possibility outdated video drivers could have caused this logic error..?? I did have a separate issue to do with /clone and /fill, serious visual artefacting as described in MC-62958, and it was fixed by updating my video drivers. It seems unlikely to me that a change in video drivers could cause a change in the way the sign-placing code behaves, but the visual glitches themselves were strange & wild in the most unlikely ways too...

I had a thought that it might be the result of multiple signs being overwritten with air in one command, but I gave that a try and it did not reproduce it. Not sure what else to try... I'd love to give you a solid repro on this one. 😛

Might be MC-73193
Could you try if you can recreate it with the command provided there?

Okay, I've just reproduced it. Here are the steps I followed:
New Superflat world, I used the Redstone Ready preset but I'm sure it doesn't matter.
Construct a column two blocks wide and 93 blocks tall. Again, exact height probably doesn't matter, I just wanted it to be in the same ballpark as my original construction. The two blocks of width should be different Z coordinates, same X.
Face the pillar facing west ("towards negative X"). Not sure if this is important, but MC-73193 mentioned it, so I decided to go with it.
Place signs every 4 blocks up the left side of the pillar (higher Z). Again, this precise detail is probably not important, but I mimicked my original design and placed a number in each sign to represent a floor number, as in my 20-storey building.
Clone the right side of the pillar (with no signs), plus the block of air in front where the signs are on the left side, overtop of the left side. All the signs disappear.
When re-placing the signs, the text that was previously assigned magically reappears.
I tried saving and re-opening the world, and the text went away, so it isn't actually persisted in the world files (or if it is, it fails to load back in).
This may be the same underlying bug as in MC-73193, but I'm reporting it in the context of a clone command that does not use the "move" clone mode.

This probably also relates to: MC-46094
You should be always able to reproduce it when using this command:
/fill ~3 ~-1 ~3 ~-3 ~-3 ~-3 air

Gave it a quick try, couldn't reproduce. Is this still an issue in 15w44b? If so, please update the list of affected versions.

I just reproduced it in 15w45a.

Can you provide a list of commands one can enter to reproduce the bug without having to manually place blocks or pay attention to orientation?

Does MC-82703 describe your issue?

Is this still an issue in the most recent versions (currently that is 1.10.2, or 16w42a) of Minecraft? If so, please update the affected versions and help us keeping this ticket updated from time to time.

Need help reproducing this in any of the originally-reported versions e.g. 15w50a.
I'm placing a sign, I'm using /fill to clear a 1x5x5 area around the sign, and I can never make this bug appear. I also tried clearing the area using /clone replace move: no luck.
What am I missing that isn't being communicated in the instructions?
Hmm, okay, I'm trying to reproduce this and haven't succeeded yet. However, I did experience it repeatedly while actually playing. I had constructed a flight of stairs for a 20-storey building, and used /clone to replicate the 2nd floor's stairs up to the 20th storey. Then, I manually placed signs indicating which floor each one was. When I tried the stairs, however, I realized there was a mechanical fault with them, so I redid them and /cloned over the space they had been in. After doing this, all the signs were gone, but when I went to re-place them, wherever they had already been before, the floor number was already there.
This happened on west-facing walls, in case that matters...