I assume that you want to remove the "first 1000 lines", given the unsorted order of the result of the "select" query without sorting arguments and no criteria, in which case you are doing something wrong.
But, as an academic exercise, here's how you do it. All rows in SQLite have a field rowidthat you can use to find where these 1000 rows end.
sqlite> create table t(s string);
sqlite> insert into t values('a1');
sqlite> insert into t values('a2');
sqlite> insert into t values('a3');
sqlite> insert into t values('a4');
sqlite> select * from t;
a1
a2
a3
a4
sqlite> delete from t where rowid < (select rowid from t limit 2,1);
sqlite> select * from t;
a3
a4
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