The tweak epub feature is in the right-click menu for any given book, or just press the letter 't' on your keyboard.
The simplest approach is just to delete every line with 'margin-left' in the css file (it's highly unlikely to exist with every style), though if there was some book content that was actually supposed to be indented you will lose that - then again you've been losing it by converting to rtf, so it probably doesn't matter.
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