Try the following.

while (<DATA>) {
    chomp;
    $rec = substr($_,0,2); $_ = substr($_,2);
    if ($rec == 10) {
        $id = substr($_,0,5); $_ = substr($_,6);
    }
    $records{$id}{$rec}{'date'} = substr($_,0,10);
    if ($rec != 50 || !exists($records{$id}{50}{'data'})) {
        $records{$id}{$rec}{'data'} = substr($_,10);
    }
    else {
        $records{$id}{50}{'data'} .= ' ' . substr($_,10);
    }
}
for (sort keys %records) {
    $id = $_;
    print "$id\n";
    for (sort keys (%{$records{$id}})) {
        print "$_ : ".$records{$id}{$_}{'date'}." : ".$records{$id}{$_
+}{'data'}."\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, by a general
5001.11.1997practitioner on not more than 1 patient
1000002 01.11.199600.00.00001 A1 1 SN Y
2001.11.200400098.0500073.5500083.35
5001.11.1997Professional attendance being an attendance at
5001.11.1997other than consulting rooms, by a general
5001.11.1997practitioner on not more than 1 patient
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