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Yeah. I've noticed it a couple of times.

For example, the text at 0:09 used to say "Envy" (previous band name) instead of "Nico & Vinz" (new band name), but they got Youtube to replace the video with a new one.

And as you can see, the Youtube video with their new name hardcoded into the video was "uploaded" half a year before they actually switched their name (Jan 2014).

https://www.youtube.com/watch?v=bg1sT4ILG0w

You can make certain changes to any video and still keep the id. E.g. any arbitrary trimming or other edits allowed by YouTube's video editor, adding annotations to the video itself etc.

OP's fear and my reply were about changes done by Google, not edits done by channel owners.

This is my thought as well. This was probably an ill thought through change. Most likely they have only done this to their own content or like you said, to other premium partners for small changes like quality issues etc.

I'm rather going to assume stressed bad ideas over deliberate dick moves.