Thanks Ludwig for your reply.
For your first point, i think the error is coming because in the old structures all the ledger accounts are define. Say like i created the structure Say, APP for ledger accounts 1-10 which have the segment main accounts and the site.Now i duplicate it with the structure APP1 by adding one more segment say like business unit. In the structure i will be activated.
Now we will move to the ledger form, which already have the APP structure and i am trying to add APP1 with out removing the APP. May be the error is coming due to that.