Need to batch convert PDF to RTF while maintaining original folder structure

I'm using Acrobat Pro 9 and I need a way to batch convert PDF files to RTF while maintaining the original folder structure.  So for instance, I might get a set of interview transcripts that were conducted with members of 1000 randomly selected households in 3 different cities.  Something like this, where the words in all caps are folder names:
BOSTON
       HH1001
            PERSON-1A
                    Interview1.pdf
                    Interview2.pdf
            PERSON-2A
                    Interview1.pdf
                    Interview2.pdf
       HH1002
            PERSON-1A
                    Interview1.pdf
                    Interview2.pdf
            PERSON-2A
                    Interview1.pdf
                    Interview2.pdf
            PERSON-1C
                    Interview1.pdf
                    Interview2.pdf
DETROIT
       HH2001
            PERSON-1A
                    Interview1.pdf
                    Interview2.pdf
            PERSON-2A
                    Interview1.pdf
                    Interview2.pdf
       HH2002
            PERSON-1A
                    Interview1.pdf
                    Interview2.pdf
            PERSON-2A
                    Interview1.pdf
                    Interview2.pdf
            PERSON-1C
                    Interview1.pdf
                    Interview2.pdf
As u can see, the folder structure can get quite complicated and it's important to keep it the same.  Is there any way I can batch convert without having to open all 1000 files at once (which would crash the computer) or without having to add each subfolder to the Export Multiple Files window?
I also tried saving the original folders and files in a portfolio and then converting the portfolio, but that puts all the converted files in a single folder.

Bernd Alheit wrote:
For the output location choose 'Same Folder as Original(s)'
Yes, I've done that many times.  It doesn't put them in the correct folder structure, it just puts all the new files in the highest-level folder.

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