I've not had a problem with the way Sigil reorganises the files in my books when I've made them, or from format shifted books out of Calibre, but I'd prefer not to reorganise commercially purchased book.
I've had a few complaints from the retailers of those books (only submit the epub to the retailer when it is sold DRM-free, as those are the only ones that I can actually change.
) when Sigil makes those changes.