You're probably thinking of the problem with some *very* old versions of CPAN.pm where it would, under some circumstances, try to upgrade your version of perl, and that can really bugger things up. However, version 1.87 is fine. I've done exactly that upgrade several times on various builds of perl, and it worked just fine. IIRC the problem was with the version of CPAN.pm distributed with perl 5.005, and was fixed in perl 5.6.0.

When you upgrade it'll use as much of your old configuration as possible, and ask you to configure any new options the first time it tries to use 'em. To change them, type 'o conf urllist ...' at the CPAN shell or (and I find this more convenient) edit CPAN/Config.pm by hand.