I'm not sure I understand the question, so please let me know if this is not an answer.
I don't know why the designer is converting the letter the way you are showing. Code128 can take alpha characters directly. If your intention is to encode 0123456789A01234B0123, then just use that after the "^FD>:"
Try modifying the prn file to something like the following:
CT~~CD,~CC^~CT~ ^XA~TA000~JSN^LT0^MNW^MTT^PON^PMN^LH0,0^JMA^PR2,2~SD22^JUS^LRN^CI0^XZ ^XA ^MMT ^PW799 ^LL0400 ^LS0 ^BY2,3,100^FT30,241^BCN,,Y,N ^FD>:0123456789A01234B0123^FS ^PQ1,0,1,Y^XZ
As for sample code, Are you using the Link-OS SDK or doing something else?
If the SDK, I have some sample code posted here: DEVTALK Wednesday, December 13th 10 AM CDT - Integrating Zebra Printers with Windows Via the New Link-OS C# SDK . Just replace the ZPL_STRING with the contents of the prn file or read the prn file into a byte and send that. If you want to use this as a template, which we do recommend, take a look at the FormatUtil Interface and the sample code GitHub - Zebra/LinkOS-PC-Samples at ZSDK_DevDemos_.NET for a full demo of template based printing.
I hope this is what you were looking for,