perl -i.bak -nle 's/search/replace/g unless $. & 2; print' file

##</code><code>##

line 1
line 2
line 3
line 4
line 5
line 6
line 7
line 8
line 9

##</code><code>##

$ perl -nle 'print unless $. & 2;' lines.txt
line 1
line 4
line 5
line 8
line 9