Yes.

I say that because there are countless examples of films with more than one version being released on dvd and blu-ray with both/all of their versions included.

I seem to remember reading an article on the official site way back in 2002 where one of the people involved with AotC (on the vfx end of things, I think) said there were like 80 little differences just between the theater version and the dvd version.* The only big noticeable difference between the 35mm and digital versions in theaters was Padme holding Anakin's hand at the end, but the longer scene of his confession about slaughtering the Tuskens ("I'm a Jedi") wasn't added until the dvd IIRC.

*It was 12 years ago now, so my memory is a bit fuzzy. The dude might've just been talking about the 35mm and digital versions. It would help if I could remember what time of year it was.