You can also process the string character by character, keeping the state (inside/outside backticks) in a flag variable. To handle unclosed backsticks, only replace the characters when you meet the closing quote, so keep a list of positions to replace in an array. Replacements are happening from the right so you don't have to recalculate the remaining positions after the length of the string changes. 
sub process {
    my ($string) = @_;
    my $inside;
    my $pos = 0;
    my @replace;
    while ($pos < length $string) {
        my $action = {
            '\\' => sub { ++$pos },
            '<'  => sub { unshift @replace, $pos if $inside },
            '`'  => sub {
                unless ($inside = ! $inside) {
                    substr $string, $_, 1, '&lgt;' for @replace;
                    $pos += 5 * @replace;
                    @replace = ();
                }
            },
        }->{ substr $string, $pos, 1 };
        $action->() if $action;
        ++$pos
    }
    return $string
}

[download]
($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,

[download]

In reply to Re^2: Replacing left angle bracket with HTML entity when between two backtick characters by choroba
in thread Replacing left angle bracket with HTML entity when between two backtick characters by nysus

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