Keep acrobat from deleting header/footer created in Word when updating Acrobat header?

I was running into the exact same problem with Acrobat X Pro and went searching for a solution. I came up with an answer from acrobatusers.com, so I thought I'd share it here:

1. In Word 2007 or Word 2010, click on the Acrobat tab in the menu bar then open Preferences.
2. On the Settings tab, uncheck Enable Accessibility and Reflow with tagged Adobe PDF.
   Convert your file to PDF.
3. Now when you add a header in Acrobat you should no  longer get the dialogue to replace existing header or add new one.

I tried this and when you open the imported Word document in Acrobat, Acrobat thinks the original Word headers and footers are "text" instead of coded as a header or footer. As stated above, you don't have the option for Remove... or Update..., but can only Add Header & Footer...

If you do add a header or footer in Acrobat, it will only allow you remove or update the Acrobat header or footer you just added, but won't touch the original Word header or footer.

Within the Add Header and Footer... dialogue -> Appearance Options -> Shrink document to avoid overwriting the document's text and graphics seems to function correctly as well, and retains the original Word header and footer when it shrinks down the document.

Was this issue ever resolved?  I am having the exact same issue.  More than 300 Word docs with headers and footers are combined into one PDF file.  I then add a PDF footer to track each page within the entire document.  When I need to add/change info, I can't update the PDF footer without striping away all the Word headers and footers.  Like each of the others that replied here, I NEED A SOLUTION AND QUICK!!!  Thanks!

I also came across this problem when doing research to figure out how to put my organization's board books (500+ pages) online for their quarterly meetings. I work with both Word and Excel files from different departments in my company that need to be combined as PDFs. My original idea was to establish headers for the original documents and leave the footers blank, adding footers when the PDF was combined. That worked well until I ran across this problem>

Since there always seems to be last-minute changes, even adding the numbers as a last step may not be an acceptable workaround, since we're never quite sure when the last step is! Trying to get people to adhere to strict deadlines is tough -- there's always someone with a reasonable (and important, of course) exception.

I tried entering this as a bug into the Adobe support system, but couldn't access that page nor the enhancement page.

This is an incredibly annoying problem that mars what would otherwise be a very good solution for us.

Susan

Similar problem here, too!  We have many documents that need to be merged together and consecutively numbered.  Each document needs a separate header.  Some of the headers were created in Word and some by the Add Header/Footer function in Acrobat 9 when the original files were PDF'd.  After files were combined, we added the footer with the consecutive page numbering.  So far so good.  Unfortunately, when a page needs to be inserted (and the footer updated), headers disappear, kind of randomly. Some of the headers that had been inserted into PDFs disappear, and most headers from Word documents disappear.

Would this be because some Word files had previously been PDF'd before they were combined? What about the PDF'd files' headers? 

Our workaround has been to save a master file without the footer until just before printing, and to insert the footer immediately before printing.  But it's kind of clunky.