You didn't clearly express what you wanted as your final structure, so I hope this helps

my %records;
my $record;

while (<DATA>) {
   chomp;

   my $line = $_;
   s/^(\d\d)//;
   my $subrecord_type = $1;

   if ($subrecord_type == 10) {
      s/^(\d+)\s+//;
      my $procedure_num = $1;
      $records{$procedure_num} = $record = [];
   }

   push(@$record, $line);
}

require Data::Dumper;
print(Data::Dumper::Dumper(\%records));

__DATA__
1000001 01.11.199600.00.00001 A1 1 SN Y
2001.11.200400098.0500073.5500083.35
5001.11.1997Professional attendance being an attendance at
5001.11.1997other than consulting rooms, by a general
5001.11.1997practitioner on not more than 1 patient


output
======

$VAR1 = {
          '00001' => [
                       '1000001 01.11.199600.00.00001 A1 1 SN Y',
                       '2001.11.200400098.0500073.5500083.35',
                       '5001.11.1997Professional attendance being an a
+ttendance at',
                       '5001.11.1997other than consulting rooms, by a 
+general',
                       '5001.11.1997practitioner on not more than 1 pa
+tient',
                     ]
        };
[download]

=== or maybe ===

my %records;
my $record;

while (<DATA>) {
   chomp;

   my $line = $_;
   s/^(\d\d)//;
   my $subrecord_type = $1;

   if ($subrecord_type == 10) {
      s/^(\d+)\s+//;
      my $procedure_num = $1;
      $records{$procedure_num} = $record = {};

      s/^(\d\d\.\d\d\.\d\d\d\d)//;
      my $date1 = $1;

      s/^(\d\d\.\d\d\.\d\d\d\d)//;
      my $date2 = $1;

      my (
         $unknown1,
         $unknown2,
         $unknown3,
         $unknown4,
         $unknown5,
      ) = split(/\s+/, $_);

      %$record = (
         date1    => $date1,
         date2    => $date2,
         unknown1 => $unknown1,
         unknown2 => $unknown2,
         unknown3 => $unknown3,
         unknown4 => $unknown4,
         unknown5 => $unknown5,
         20       => [],
         30       => [],
         40       => [],
         50       => [],
      );

      next;
   }

   if ($subrecord_type == 20) {
      s/^(\d\d\.\d\d\.\d\d\d\d)//;
      my $date = $1;

      my (
         $unknown1,
         $unknown2,
         $unknown3,
         $unknown4,
      ) = split(/\./, $_);

      push(@{$record->{20}}, {
         date     => $date,
         unknown1 => $unknown1,
         unknown2 => $unknown2,
         unknown3 => $unknown3,
         unknown4 => $unknown4,
      });

      next;
   }

   if ($subrecord_type == 30) {
      # ...
      next;
   }

   if ($subrecord_type == 40) {
      s/^(\d\d\.\d\d\.\d\d\d\d)//;
      my $date = $1;

      push(@{$record->{40}}, {
         date => $date,
         text => $_,
      });

      next;
   }

   if ($subrecord_type == 50) {
      s/^(\d\d\.\d\d\.\d\d\d\d)//;
      my $date = $1;

      push(@{$record->{50}}, {
         date => $date,
         text => $_,
      });

      next;
   }
}

require Data::Dumper;
print(Data::Dumper::Dumper(\%records));

__DATA__
1000001 01.11.199600.00.00001 A1 1 SN Y
2001.11.200400098.0500073.5500083.35
5001.11.1997Professional attendance being an attendance at
5001.11.1997other than consulting rooms, by a general
5001.11.1997practitioner on not more than 1 patient


output
======

$VAR1 = {
          '00001' => {
                       'date1' => '01.11.1996',
                       'date2' => '00.00.0000',
                       'unknown1' => '1'
                       'unknown2' => 'A1',
                       'unknown3' => '1',
                       'unknown4' => 'SN',
                       'unknown5' => 'Y',
                       '20' => [
                                 {
                                   'date' => '01.11.2004',
                                   'unknown1' => '00098'
                                   'unknown2' => '0500073',
                                   'unknown3' => '5500083',
                                   'unknown4' => '35',
                                 }
                               ],
                       '30' => [],
                       '40' => [],
                       '50' => [
                                 {
                                   'date' => '01.11.1997'
                                   'text' => 'Professional attendance 
+being an attendance at',
                                 },
                                 {
                                   'date' => '01.11.1997'
                                   'text' => 'other than consulting ro
+oms, by a general',
                                 },
                                 {
                                   'date' => '01.11.1997'
                                   'text' => 'practitioner on not more
+ than 1 patient',
                                 }
                               ],
                     }
        };
[download]