Throwaway account here. I had this same exact problem and finally found a solution that worked. I am posting my answer here in case anyone else has this same problem and stumbles across this article.
Here is my situation. The ultimate product I want is a very large pdf. This pdf will have a footer with a distribution statement and page numbers. This large pdf is compiled from individual pdf attachments. For me, I have some word documents with a header. I converted this word doc into a pdf. This pdf was then one of the several attachments in my final pdf document. In my final pdf document, I am able to successfully add a footer to the report. However, if I wanted to edit the footer at all, it would remove every single header in the pdf attachments that were created from word documents. It didn’t affect any other header, except the headers that were present in any word documents I converted to pdf. Also, I am positive that the header margin widths were correct and should not have removed my header.
Solution -
In my word document (2013 for me), to convert it into pdf form, I had to go to File -> Save as Adobe PDF. I then click the Options box. For the checkboxes, make sure that the only checkbox is Convert document information. Then save the file.
Now when I compiled all my multiple pdfs into a single pdf document, I am able to successfully add a new footer with page numbers and a little distribution statement. And I am also able to change the footer if necessary without it affecting any of my headers.
I have found through trial and error that going to File -> Save As – And then saving it as a pdf gave me the same problem that the Op had.
I really hope if anyone is reading this with the same problem, that I am able to save some frustration.