Flintoff came into the championship picture for the clash with Hants at Southampton, but next week joins the England Under 19 squad of which he is captain for the series against the Zimbabwe tourists.
The youngster launched Lancashire's championship revival with a match-winning performance at Worcester, and he is now the automatic replacement for John Crawley when England are in action.
But his under 19 duties mean he will be unavailable for two championship matches in August when Crawley is involved in the fifth and sixth Tests.
The under 19s series has infuriated Surrey coach Dave Gilbert who loses Ben Hollioake, but Lancashire have made no complaint about Flintoff.
Lancashire also called up Nathan Wood today to fill the gap left by Mike Atherton as they aimed for their fourth championship win on the trot. The last time they achieved that sequence was in 1991.
Coach Dav Whatmore said: ``We are just taking a small step at a time.'' Jason Gallian and Nathan Wood were unbeaten at 14 from six overs.