Since this requires users of your code to change their code, I would avoid making it not obvious what has happened.
You could replace the old namespace functions with wrappers that call the new functions for backwards compatibility - but then, what have you ultimately gained? Two things to update instead of one.
With things like these, just do it, tell people that the old code is deprecated (especially in the perldoc and on CPAN) and leave it up to them if they ever want to upgrade and fix their code, and then ignore the old version.
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