This will read 6 lines, then let you do something else then return to reading another 6 lines until the end of the file. (start up code and Template code omited as the former is not changed and I don't know any thing about the latter =)

...
until (eof(FH)) {
    for my $i (1..6) {
        my $line = <FH>;
        last unless defined $line;
        chomp $line;
        redo if ($line =~ /^\s*(?:#|$)/);
        if ($line=~m#(map|reverse_map)\s+(\w+)://(\S*?)\s+(\2)://(\S*?
+)$#) {
            $vars{'d'}     = $.;
            $vars{'map'}   = $1;
            $vars{'proto'} = $2;
            $vars{'uri1'}  = $3;
            $vars{'uri2'}  = $4;
        }
    } #do some thing with $vars before here.
    #6 lines (or as many as remained in the file) will have been read 
+at this point 
}
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