Try this:
delete from your_table;
delete from sqlite_sequence where name="your_table";
SQLite keeps track of the largest
ROWID that a table has ever held using
the specialSQLITE_SEQUENCE
table. The
SQLITE_SEQUENCE
table is created and
initialized automatically whenever a
normal table that contains an
AUTOINCREMENT column is created. The
content of the SQLITE_SEQUENCE table
can be modified using ordinary UPDATE,
INSERT, and DELETE statements. But
making modifications to this table
will likely perturb the AUTOINCREMENT
key generation algorithm. Make sure
you know what you are doing before you
undertake such changes.