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

my $file1=<<END;
"A123","valueA1","valueB1"
"B234","valueA2","valueB2"
"C345","valueA3","valueB3" 
"D456","valueA4","valueB4"
"E567","valueA5","valueB5" 
"F678","valueA6","valueB6"
END

my $file2=<<END;
"C345","valueX1","valueY1"
"D456","valueX2","valueY2"
END

my %hash;

# read file1 into a memory hash table

open (FILE1, '<', \$file1) or die "$!";
while (my $line = <FILE1>)
{
   chomp $line;
   my ($key,@vals) = split ',',$line;
   $hash{$key} = [@vals];
}

# process file2, modify the memory hash table

open (FILE2, '<', \$file2) or die "$!";
while (my $line = <FILE2>)
{
   chomp $line;
   my ($key,$val1) = split ',',$line;
   $hash{$key}[0] = $val1 if $hash{$key};
}

# dump the hash table

foreach my $key (sort keys %hash)
{
   print "$key,", join(",",@{$hash{$key}}),"\n";
}

__END__
Prints:

"A123","valueA1","valueB1"
"B234","valueA2","valueB2"
"C345","valueX1","valueB3" 
"D456","valueX2","valueB4"
"E567","valueA5","valueB5" 
"F678","valueA6","valueB6"