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There are several possibilities how this situation can be handled.
As I understand, we have a repetition of the same pages, which are made available to he end user, and not a recombination of individual forms.
In this case, you could use Page Templates, where you mark the pages which may occur more than once as a Template. You then spawn these Template pages with the field renaming option switched on. This will add a prefix to the field names on a given spawned page, making them unique. If you have "common" information, you can prefill before spawning, and leave the individual fields blank.
This is therefore the preparation approach.
If you have already filled forms, and want to recombine them (but no longer have the fields editable, you would flatten the documents, and then recombine.
Finally, if you want to do a mass-prefilling, you could use a specially crafted FDF file containing the data, and working with Template pages (this would, however, create individual files, which would not have unique field names).
FWIW, "refrying" (sending a PDF through a PostScript printer driver and recreate the PDF using Distiller) is something you only should do when you really know what you are doing.
Best Answer
You can install a 'PDF printer'. That is a virtual printer. Printing to it asks you for a filename and the result ends up in a PDF file.
Printing to such a PDF printer strips all field functionality.
The one I personally use is pdfcreator, but there are many similar programs.
Warning: Should you test the one I linked to, make sure you untick the 'helpful software' bar. Do not just [next][next][next][Finish].