This is why I convert my books one by one. You can explode the epub in Calibre then edit the style sheet using a free editor like Topstyle light, Notepad2, PSpad or Notepad++ I use Topstyle as I'm an ole web Designer so it's my tool of choice when doing style sheets.
I usually check the ignore margin option first but if that doesn't work I edit the style sheet directly.
For indentation I use:
p {text-indent:1.3em;}
in the Extra CSS box.
It works in most cases "p" being the class that paragraphs use. Some use Div tag instead so you may have to edit it whatever class/tag the book uses to mark paragraphs.
Calibre now removes fake indentation. It saves a step of having to remove it manually in Search & Replace when it's coded in the actually html of book and not the style sheet.
