If the substitution doesn't match, then the substitution is not performed, so all you need to do is combine the two one liners that you have into one:

perl -pi -e's/^(66.11.10.20)/#$1/g' ips.txt
[download]

Now then, stepping through the list of IP addresses is another issue. I would recommend using a script for this rather than a one liner.

Update: i'm sticking to my case, but this is too much fun. :) Let's say you have 2 text files, one containing the list of all IP addresses (all_IPs.txt) and another containing a smaller list of IP addresses to be commented out in the first text file (decomission_IPs.txt). You could use the shell to create individual strings that contain the Perl one-liners that can in turn be fed back to a shell:

for i in `cat decomission_IPs.txt`; do perl -le $"print 'perl -pi -e \
+'s/^(\Q$i\E)/#\$1/g\' all_IPs.txt' "; done | sh
[download]

L-LL-L--L-LL-L--L-LL-L--
-R--R-RR-R--R-RR-R--R-RR
B--B--B--B--B--B--B--B--
H---H---H---H---H---H---
(the triplet paradiddle with high-hat)