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In the Preferences (Edit -> Preferences) there is a Warnings section. See if you unchecked anything in there that might be related.
It's the first place where i tried to fix the problem but it is not.
There is no more warning section in the preference...
There is well a "reset warnings" button, but it is grey (inaccessible)
Where are the good old CS preferences, by the way !
For the point you noticed :
It already happens to me, when the symbol I am replacing is exactly the same. When working on different version of the same file, for instance. Then there is no warning.
I guess it has to be some xml-file with settings including this duplicated names warning, but where it is is a question))