You didn't provide the second JSON, so I had to hallucinate one myself. The comment shows where you need to adjust your code.

The basic idea is to index the first json by the external id using a hash.

#!/usr/bin/perl
use warnings;
use strict;
use experimental qw( signatures );

use Cpanel::JSON::XS qw{ encode_json decode_json };
use List::Util qw{ shuffle };

sub create_json1($name, $size) {
    my @watchers;
    for my $i (shuffle(1 .. $size)) {
        push @watchers, { externalId => $i,
                          watchers => [map "$_",
                                       map 1 + int rand $size, 0 .. ra
+nd 4] };
    }
    open my $out, '>', $name or die "$name: $!";
    print {$out} encode_json(\@watchers);
}

sub create_json2($name, $size) {
    my @list;
    for my $i (shuffle(1 .. $size)) {
        push @list, { id => $i };
    }
    open my $out, '>', $name or die "$name: $!";
    print {$out} encode_json(\@list);
}

sub merge ($name1, $name2) {
    open my $in1, '<', $name1 or die "$name1: $!";
    my $struct1 = decode_json(do { local $/; <$in1> });
    open my $in2, '<', $name2 or die "$name2: $!";
    my $struct2 = decode_json(do { local $/; <$in2> });

    my %by_id = map { $_->{externalId}, $_->{watchers} } @$struct1;
    for my $member (@$struct2) {
        # This depends on the structure of the 2nd file.
        if (exists $by_id{ $member->{id} }) {
            $member->{watchers} = $by_id{ $member->{id} };
        } else {
            warn "$member->{id} not found in $name1";
        }
    }
    print encode_json($struct2);
}

my $SIZE = 100_000;
create_json1('1.json', $SIZE);
create_json2('2.json', $SIZE);
merge('1.json', '2.json');
[download]

Runs under 2 seconds on my old machine.