It seems you want to define the parsing schema as
<Rootnode>
<Header> (0,1)
<Data> (0,1)
<Trailer>(0,1)
So your batch is the whole file and each individual XML instance will either be a header, a data or a trailer record.
Then ignore the header and trailer in your application. This obviously does not preserve your integrity check, but it parses the instances like you want.
Hope that is useful
– weak architect