Put all the data you'll need in $allkeys and then just pull it all out with values.

my $allkeys;
for  ( @{ $allusers } ) {
    my $user = $_->{'user'};
    if ( !exists $allkeys->{$user} ) {
        $allkeys->{$user} = { %{ $_ } };
    } else {
        my $refAttributes              = $allkeys->{$user};
        $refAttributes->{'amount'}     += $_->{'amount'};
        $refAttributes->{'duration'}   += $_->{'duration'};
    }
}

my $finalArray = [ values %{ $allkeys } ];
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