You can delete the old ones. However, once done, you need to ensure that you have all the perl modules you need, so:
rm -Rfv /home/.cpan/
/usr/local/cpanel/bin/checkperlmodules
Keep running checkperlmodules until it runs cleanly (i.e. no more module updates).
For good measure you may have to reinstalled exim too as it has some perl module dependencies:
/scripts/eximup --force