It should not matter how the fonts are embedded, as long as they are embedded, your RIP/printer should be able to render the pages without any problems. Any PDF file that was valid when you create it with Distiller 6 is still a valid PDF file.
If you really want to process these documents, then Acrobat would not be the tool to do it: 50K documents is a bit more than the automation features in Acrobat can handle. You may wan to look at something like Enfocus PitStop Server, or Callas' pdfToolbox. The way this would work is that you would un-embed any embedded font, and then re-embed the new font.
What you want to do may however not work - your success will depend highly on the PDF files.