Most of us have 2 copies of the image. One copy is archived in some way and not touched. It would seem quite reasonable then to leave the master image (which in my process is the first of two images I make, but which could also be an archive of your original image) the way it was, and use a tool like FTK Imager to "image" your working image and make a copy with the information presented in the way that you desire. (Note I'm talking about imaging the logical content of the E01 file, not imaging the whole file container with the metadata and such.) Since you're making a reproducible transformation of your working image, and you document it, there's no problem with integrity so long as the MD5 of the actual source drive content matches.
Of course, I always create DD images, so I'd never have this issue.