Well, if you're determined enough to try and fix it yourself, it should be pretty easy.
You will need to strip the DRM and unpack from Mobipocket to HTML, but from what I've seen of the source files from the sample, all you'll have to do after that is do a find/replace in your favourite text editor to change all the <font size="#"> to have the same consistent number and then regenerate the .mobi.
No need to fiddle with anything else and if you can set the metadata so that the fixed file has the same ASIN identifier number as the original, then apparently Amazon will even back up your notes and highlights on it to their server, too.
Of course, this may be more than you want to bother with for a relatively minor problem in what sounds like an otherwise well-done book.
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