There's always some—for example, the new file could end up written to a bad disk sector and you fail to notice before deleting the original.
That said, I've never noticed any actual loss. Sometimes CSS gets changed or the file structure. Personally, if I'm going to be doing any heavy modifications, I like to copy the original ePub to a backup folder.
In the Calibre GUI at least, you can do an ePub > ePub conversion and skip the intermediary; in this case it'll also produce an ORIGINAL_EPUB and a option to compare them. I'm not sure if web has the same.