Here's a solution that does what you're after. The substitution is:

s{\[\[(.*?)\]\]}{$1 =~ s/ /_/gr}e
[download]

I've added an additional test to check that various embedded brackets do not cause issues.

$ perl -Mstrict -Mwarnings -E '
my $x = q{Here are [[a variable number of words]] in brackets};
say $x;
$x =~ s{\[\[(.*?)\]\]}{$1 =~ s/ /_/gr}e;
say $x;
my $y = q{Here are [[a variab]le number [ of ] wo[rds]] in brackets};
say $y;
$y =~ s{\[\[(.*?)\]\]}{$1 =~ s/ /_/gr}e;
say $y;
'
Here are [[a variable number of words]] in brackets
Here are a_variable_number_of_words in brackets
Here are [[a variab]le number [ of ] wo[rds]] in brackets
Here are a_variab]le_number_[_of_]_wo[rds in brackets
[download]

Ah - I forgot you could do s/// on $1 - I guess the /r switch allows you to do it as it doesn't modify $1. Thanks, good call. I'll check it's supported on my version of perl.

> I guess the /r switch allows you to do it as it doesn't modify $1. Thanks, good call. I'll check it's supported on my version of perl.

If not try this instead:

my $x = q{Here are [[a variable]] number [[of words]] in brackets};
say $x;
$x =~ s{\[\[(.*?)\]\]}{ (my $x=$1) =~ s/ /_/g; $x }ge;
say $x;
[download]

added a /g to allow multiple chunks to be processed.

Here are [[a variable]] number [[of words]] in brackets
Here are a_variable number of_words in brackets
[download]

But to improve readability I would rather opt against one-liner and call a function in the replacement part

sub blank2under {
  my $x=shift;
  $x =~ s/ /_/g;
  return $x;
}
[download]

Cheers Rolf

update

and here a generic function to simulate /r

sub rx (&$) {
  my $c_regex=shift;
  local $_=shift;   
  $c_regex->();
  return $_
}

my $x = q{Here are [[a variable]] number [[of words]] in brackets};
print "$x\n";
$x =~ s(\[\[(.*?)\]\])( rx {s/ /_/g} $1 )ge;
print "$x\n";
[download]