It would be interesting to know how the files are ordered. Your post implies that the second file is in the same order as the first, but with gaps, and your response to Perlbotics says that you need to maintain the same order. This code seems to do that with the data you've provided.

use strict;
use warnings;

use Data::Dumper;

open my $firstFH, q{<}, \ <<END1 or die qq{open: < HEREDOC: $!\n};
DISTINGUERE TRA;1;14;507;0,000000242475382686773;0,0000033946553576148
+2;0,000122935019022194;0,00000000041732202096217;9,18246152003019;9,1
+8246152003019
MANCANTE DI;1;56;507;0,000000242475382686773;0,0000135786214304593;0,0
+00122935019022194;0,00000000166928808384868;7,18246152003019;7,182461
+52003019
APPLICARE SU;1;64;507;0,000000242475382686773;0,0000155184244919535;0,
+000122935019022194;0,00000000190775781011278;6,9898164420878;6,989816
+4420878
MONTATO IN;1;78;507;0,000000242475382686773;0,0000189130798495683;0,00
+0122935019022194;0,00000000232507983107495;6,70441422322555;6,7044142
+2322555
IMPIEGATO IN;2;180;507;0,000000484950765373545;0,0000436455688836191;0
+,000122935019022194;0,00000000536556884094218;6,49796334575812;12,995
+9266915162
RAGGRUPPARE IN;1;109;507;0,000000242475382686773;0,0000264298167128582
+;0,000122935019022194;0,00000000324915002034832;6,22163211731087;6,22
+163211731087
END1

my @order = ();
my @arr1  = ();
while( <$firstFH> )
{
    chomp;
    my( $col1, $lastVal ) = ( split m{;} )[ 0, -1 ];
    push @order, $col1;
    push @arr1, $lastVal;
}

close $firstFH or die qq{close: < HEREDOC: $!\n};

open my $secondFH, q{<}, \ <<END2 or die qq{open: < HEREDOC: $!\n};
DISTINGUERE TRA;1;14;507;0,000000242475382686773;0,0000033946553576148
+2;0,000122935019022194;0,00000000041732202096217;9,18246152003019;9,1
+8246152003019
APPLICARE SU;1;64;507;0,000000242475382686773;0,0000155184244919535;0,
+000122935019022194;0,00000000190775781011278;6,9898164420878;6,989816
+4420878
MONTATO IN;1;78;507;0,000000242475382686773;0,0000189130798495683;0,00
+0122935019022194;0,00000000232507983107495;6,70441422322555;6,7044142
+2322555
IMPIEGATO IN;2;180;507;0,000000484950765373545;0,0000436455688836191;0
+,000122935019022194;0,00000000536556884094218;6,49796334575812;12,995
+9266915162
END2

my $idx  = 0;
my @arr2 = ();
while( <$secondFH> )
{
    chomp;
    my( $col1, $lastVal ) = ( split m{;} )[ 0, -1 ];
    if( $col1 eq $order[ $idx ] )
    {
        push @arr2, $lastVal;
    }
    else
    {
        push( @arr2, q{0} ), $idx ++
           until $col1 eq $order[ $idx ];
        push @arr2, $lastVal;
    }
    $idx ++;
}
push @arr2, q{0}
   until scalar @arr1 == scalar @arr2;

close $secondFH or die qq{close: < HEREDOC: $!\n};

print Data::Dumper->Dumpxs(
   [ \ @arr1, \ @arr2 ],
   [ qw{ *arr1 *arr2 } ]
   );

print
   q{[} .
   join( q{; }, @arr1 ) .
   qq{]\n[} .
   join( q{; }, @arr2 ) .
   qq{]\n};
[download]

The resultant arrays output using Data::Dumper.

@arr1 = (
          '9,18246152003019',
          '7,18246152003019',
          '6,9898164420878',
          '6,70441422322555',
          '12,9959266915162',
          '6,22163211731087'
        );
@arr2 = (
          '9,18246152003019',
          '0',
          '6,9898164420878',
          '6,70441422322555',
          '12,9959266915162',
          '0'
        );
[9,18246152003019; 7,18246152003019; 6,9898164420878; 6,70441422322555
+; 12,9959266915162; 6,22163211731087]
[9,18246152003019; 0; 6,9898164420878; 6,70441422322555; 12,9959266915
+162; 0]
[download]

I hope this is helpful.

Cheers,

JohnGG