SPECIAL THANKS go to Kevin Lossner (www.translationtribulations.com) for his help developing this workaround.
Context: you customer needs a "Trados-compatible bilingual doc" (aka "uncleaned" document) delivered, and said document contains footnotes.
By default, memoQ's bilingual doc filter will not deal with footnotes in such documents.
• Prepare the file
The workaround here is to "prepare" your source file either using Trados Workbench (not available for download anymore) or Wordfast Classic (the free trial available here will do just fine).
Using those, you need to pre-segment your file and copy source text to target side.
For both tools, you will find a nice video tutorial on Dominique Pivard's CATGuru blog, here.
• Import in memoQ
Once you have the prepared and presegmented file, in your memoQ project, import it using "Import with options" (memoQ 6 and later) or "Add document as" (memoQ 5).
The advanced Document import options will be shown:
Here, the trick is to chose another filter than the bilingual one offered by default. Simply import that document as a "normal" Word document using the default options. Do NOT import hidden text.
With that process, you fool memoQ into working on the target text only, that one being a mirror of the source text because of the way you prepared the file.
Translate in memoQ as usual and export as a standard file too (do NOT export as bilingual).
And voilà! you've got your perfectly compatible bilingual doc with footnotes.