Is there a provision to save the PDF once the remap is completed?
When you click the "OK" button on the font encoding dialog the remappings that you have set are automatically saved to the Infix preferences file and will be automatically loaded the next time you open Infix.
If you have made additional edits to the PDF file then you can just save it using "Save" or "Save As" via the "File" menu item
It is not currently possible to "Fix" the pdf mappings using Infix so that when the document is loaded into a third party application and extracted it extracts correctly.
Although if you edit the character-to-unicode mappings in Infix, Infix will be able to extract the document to other formats correctly.
In other words the answer to initial question is
NO, Infix can NOT save back to PDF with remapped fonts.
And then I ask: WHY? It is a very desired, vrry useful feature...