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my %free_days_left;
while (<$file1>) {
     chomp;
...
     my $key = join "-", @fields[0..2];
     $free_days_left{$key} = $fields[5];
}

while (<$file2>) {
     chomp;
     my @fields = split /\s+/, $_;
...
     my $corrected_duration = exists $free_days_left{$key}? $duration 
+- $free_days_left{$key} : $duration;
     print $file3 join " ", $_, $duration, $corrected_duration, $corre
+cted_duration * $unit_price, "\n";
}