Dealing with non-unique footnote numbers in markdown

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I have a markdown file where the footnote numbers restart for every chapter 
giving me non-unique footnote numbers and therefore warnings when 
processing MD->EPUB

I would like to know whether anyone has a simple method of renumbering the 
footnotes so that they are unique.

I'm using Ubuntu, and what I've done so far is to use 'csplit' to break the 
file into chapters, then 'sed' to find and prefix each footnote and 'cat' 
to append the whole thing back together again. 

Does anyone know of a simpler method for renumbering non-unique footnote 
numbers?

Many thanks for any help.

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