The RootFolder attribute on the Batch element controls the folder of the item. This can be used to access a sub-folder. The structure is Lists/list/folder where folder is optional.

For example, if the list being updated is Contacts and there are two sub-folders Work and Personal. To update an item in the Contacts list:

<Batch OnError="Continue" PreCalc="TRUE" ListVersion="0" RootFolder="/Lists/Contacts">
<Method ID="1" Cmd="Update">
<Field Name="ID">47821</Field>
<Field Name="RefID">479485</Field>
<Field Name="CustomerNumber">59613</Field>
</Batch>

And to update an item in the Work folder:

<Batch OnError="Continue" PreCalc="TRUE" ListVersion="0" RootFolder="/Lists/Contacts/Work">
<Method ID="1" Cmd="Update">
<Field Name="ID">47821</Field>
<Field Name="RefID">479485</Field>
<Field Name="CustomerNumber">59613</Field>
</Batch>