It seems to me that in order to preserve the unique values of the duplicate keys, storing an array of such values inside the hash against its key should be a candidate solution:

#!/usr/bin/perl

use Data::Dumper;
simple_call( uniq1 => 1, uniq2 => 2, dup1 => 3, dup1 => 4 );
sub simple_call { 
    my %hash = ();
    for ( my ($key, $value); $key = shift; ) {
        $value = shift;
        if ( dupAllow( $key ) ) {
            unless ( $hash{ $key } ) {
                my @tmp = ();
                $hash{ $key } = \@tmp;
            }
            my $aref = $hash{ $key };
            push @$aref, $value;
        }
        else {
            $hash{ $key } = $value;
        }
    }

    print Dumper( \%hash );
    # continue subroutine processing
    
}

sub dupAllow {
    my $key = shift;
    ( $key eq 'dup1' ) and return 1;
    ( $key eq 'dup2' ) and return 1;
    return 0;
}
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Output:

$VAR1 = {
          'dup1' => [
                      3,
                      4
                    ],
          'uniq1' => 1,
          'uniq2' => 2
        };
[download]