Lines on Contract Deleted in Application but Still in database

We have an issue where we are unable to QA Check a contract.  It is saying a item is required for the line.  The only thing is that the line that they are referring to does not exist on the contract in the form.  The contract was copied from another one and lines were deleted from the contract.  The lines are deleted from the application (they no longer are appearing) but they still exist in the database.  The contract has thousands of lines and cannot be redone.  Anyone else run across this problem and if so how do we resolve