I'm not entirely sure if I understand your Problem. It is hard to tell when you are talking in terms of text replacement and when you mean actual Perl code. I believe that dragonchild has throroughly misunderstood the problem for the same reason.

Here is one way to do what I think you want to do:

@result = map {
    my ( $x, $y) = split /=#?/;
    /=#/ ? ( $x, fn( $y)) :
    /=/  ? ( $x, $y) :
    ( $x, fn( $x));
} split /,/, $string;
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See how the code makes the map block a comfortable place, with named lexicals for the parts we work with. The nested ?: can then be written strightforward.

I think an approach more along the lines of dragonchild's (though he solved different problem) would be more readable and maintainable.

Anno

Update: Corrected misattribution to imp