while ( $javacode =~ s{ (/\*\* .*? \*/) }{ <!--REPLACED_COMMENT--> }xms ){
   push @comments, $1;
}

my @lines = ();
LINE:
foreach my $line (split "\n",  $javacode) {
   push @lines, $line;
   next LINE if $line =~ m { \A \s* // }xms;
   # change lines
   $lines[-1] =~ ...
}

$javacode = join "\n", @lines;
my $comment_id = 0;
$javacode =~ s{<!--REPLACED_COMMENT-->}{$comment[$comment_id++]}eg;