If you need the final PDF to have the requisite well-formed structure tree (that is, compliant with ISO 14289-1, PDF/UA-1) and thus "accessible" then you need to do the adjustments to your PDF's content streams before establishing that well-formed structure tree.
Note that PDF versions 1.4 or above can have that well-formed structure tree - put another way PDF version 1.4 or PDF-1 (PDF is the ISO Standard ISO 32000-1) can have the well-formed structure tree. I can 'build' such a PDF that starts as PDF version 1.4 via Acrobat 5, do some additional post-processing with Acrobat XI Pro which, via a Save As puts the PDF into a new "version" and *not* adversely affect content streams / structure tree. Your post-processing is what is changing the "guts" not the save to a different version.
Just becaues - an obtw:
For those who desire to / need to provide accessible PDF success is predicated in having and understanding the essential reference material.
ISO 32000-1 (14.8 in particular).
Document Management – Portable Document Format – Part 1: PDF 1.7, First Edition
Adobe (Jul 2008)
This document is an ISO approved copy of the ISO 32000-1 Standards document. By agreement with ISO, Adobe Systems Incorporated is allowed to offer this version of the ISO standard as a free PDF file on their own Web site.
It is not an official ISO document but the technical content is identical; the page and section numbers are also preserved.
ISO 14289-1 (PDF/UA-1)
This you will have to purchase ($104) from the ANSI Web Store.
The Matterhorn Protocol.
The resources for Accessible PDF at the AIIM site.
PDF/UA-1 Technical Implementation Guide: Understanding ISO 14289-1 (PDF/UA-1)
PDF/UA-1 Technical Implementation Guide: Understanding ISO 32000-1 (PDF 1.7) (under development)
Achieving WCAG 2.0 with PDF/UA
(WCAG 2.0 for PDF IS PDF/UA-1)
You can use Acrobat Pro to save to whatever version of PDF/A you need. If anything in particular is forbidden in PDF/A it will convert it.
Thank you to BOTH "Test Screen.." and CTDave...