I think there are two sets of material being discussed here: the "Dune 7" material, and Frank's source material for the original 6 books.
The Leto/Jessica meeting (whether for the movie or a scene in a book) would exist in the latter, which I firmly believe exists. in "The Road to Dune", I recall mention of hundreds (thousands?) of pages of source material (found in Brian's garage/attic/whatever). That's plausible. Not that they used a fraction of it in RtD, but anyhoo ...
Any alternate scenes in these notes would not be canon, IMHO, if they contradict what's in the published books.
The Dune 7 material is more doubtful. From House Atreides:
A scant two weeks after our meeting, I received a telephone call from an estate lawyer who had handled matters involving my mother and father. He informed me that two safety-deposit boxes belonging to Frank Herbert had turned up in a suburb of Seattle, boxes that none of us knew existed. I made an appointment to meet with the bank authorities, and in an increasing air of excitement the safety-deposit boxes were opened. Inside were papers and old-style floppy computer disks that included comprehensive notes from an unpublished DUNE 7 -- the long-awaited sequel to CHAPTERHOUSE: DUNE! Now Kevin and I knew for certain where Frank Herbert had been headed, and we could weave the events of
our prequel into a future grand finale for the series.
From this it's unclear whether the "papers" included the Dune 7 material, or whether it was just the disks that did. Regardless, the Dune 7 material is described as "comprehensive notes".
This flatly contradicts the account Brian gives in the Hunters audiobook interview, in that he says the "outline" contained just "hints and clues", and was 2 or 3 pages long. Not "comprehensive".
Similarly, the "35 pages" cannot refer to the outline, nor to the original source material. It's possible
that the Dune 7 material contained both notes and and outline, but then it's odd that Brian didn't mention the notes in the Hunters interview.
Personally, I believe the 2-3 page outline probably exists, and that it included just a bunch of plot ideas in no particular order. I think KJA/BH probably ignored as much of that outline as they used.
Finally, it's worth noting that in the case of Omnius, they have admitted that he is completely their own invention, and that they shoehorned him into Dune 7.