If I have understood your requirement correct
File Adapter (XML file with base64 pdf and order details) --> PI --> IDOC Order XML to R/3 using IDOC adapter
You can have to receivers for above scenario with a split mapping 1) IDOC 2) File system
For File System receiver you could use a java mapping to read base64 data and then decode to write it to outputstream (TransformationOutput) and the rest file adapter will take care. You can also a use graphical mapping with UDF to create PDF attachment and then use standard SAP payload swapbean in File receiver channel to swap main payload with PDF attachment
Best Regards,
Praveen Gujjeti