This is UNTESTED but it may help get you started:

#!/usr/bin/perl
use warnings;
use strict;

my $file2 = 'File2';

open my $IN, '<', $file2 or die "Cannot open '$file2' $!";

my %data;
while ( <$IN> ) {
    next unless /^([^=]+)=(.+)/;
    $data{ $1 } = $2;
    }

close $IN;

( $^I, @ARGV ) = ( '.bak', 'File1' );

while ( <> ) {
    s/(\@([^\@]+)\@)$/ exists $data{ $2 } ? $data{ $2 } : $1 /e;
    print;
    }
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