Yes, that's proved a pretty big problem for me because unfortunately I converted a lot of my books when I first started and lost nearly all my section breaks. It's a pity those aren't marked up consistently in all books with characters or a break code instead of paragraph codes. The upside of my mess-ups is that I've go to know Calibre and Sigil a whole lot better.
By the time I've finished wading through all my books I will be half educated.
Yes, you guessed, after a superficial glance to make sure lines had been removed and indents added I deleted the original-epubs. That was some time ago - I've only just discovered the extent of the damage I've done after reading several converted books.