A simple approach is to loop through the lines and start a new record each time a primary key is detected:

my %record;
my $item;
while (my $line = <DATA>) {
   chomp $line;
   if ($line =~ /^(\d+) (.*)$/) {
      $item = $1;
      $record{ $item} = " $2";
   }
   else {
      $record{ $item} .= $line;
   }
}

foreach my $item (keys %record) {
   print "$item $record{ $item}\n";
}

__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
1000002 01.11.199600.00.00001 A1 1 SN Y
2001.11.200400098.0500073.5500083.35
5001.11.1997Professional attendance being an attendance at
5001.11.1997consulting rooms
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