Something like this perhaps:

$ cat 1028930_short
2
5
6
8
[download]

$ cat 1028930_long
1
2
3
4
5
6
7
8
9
[download]

$ perl -i -nE 'chomp; if ($s) { $d{$_} or say } else { ++$d{$_}; ++$s 
+if eof; say }' 1028930_short 1028930_long
[download]

$ cat 1028930_short
2
5
6
8
[download]

$ cat 1028930_long
1
3
4
7
9
[download]