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Well, this message shouldn't appear if players are using HD+ 3.662 or later. I understand that it's unpleasant when something like this pops up, and you want to complain. But is it really that hard to report at least the HD version in which this happened?
If the game was started on HD+ 3.662 or later, and continued on HD+ 3.661 or earlier, then yes, this kind of thing will appear.
But if it was started and continued on HD+ 3.662 or later, then it's a bug, and it shouldn't happen.
In any case, the appearance of this window is not related to desynchronization at all! And it's generally harmless (except that it's annoying and irritating).
Since I can't reproduce the situation described above, I'm asking for a save file that causes this message to appear after loading it.