In FineReader Server 14 you have a possibility to split the pages flow by multiple barcode types using regular expressions.
For example, the following regular expression will allow you to split pages by barcodes starting with HY and barcodes starting with GT:
Read more about Regular Expressions.
To set this option up, go to workflow properties, choose the option Start new document after barcoded page and type in regular expressions for barcodes that you need to split the pages with:
Tip: the documents will be named according to barcodes that were used to split them if you choose the naming rule in the Output tab: