I had a similar issue. I ended up deleting the whole series from Amazon and my devices, re converting them (in my case mobi to mobi using Calibre) and then uping them to Amazon again. In Calibre (for instance) you can number each book in the series and when downloaded on to your PW you'll be able to see them listed as {author, series #, title} or any other way you'd like them sorted.
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