Sorry for the delay in answering you.
I did not have any inconvenient end of line hard breaks when I used FineReader with an HTML output. I only get paragraph breaks, and that's why I say that an HTML output is very flexible.
So maybe, you should look carefully at your source. If it already includes end of line hard breaks, then probably, there is nothing FineReader + HTML can do.
I do not use Microsoft Word but OpenOffice 3.1 to deal with the HTML output coming from FineReader.
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