There were TWO EOTS's. The first one was rejected at mid-levels of the Air Staff apparently by Gen Craigie in mid-Aug 1948. It was probably very short, very possibly just several pages. Keyhoe saw this version in late 1952, he recalled it was only about 3 pages, and it was stamped as having been received at AF HQ on Aug 5, 1948, signed by two AMC colonels as he told me himself when I interviewed him (the colonels were obviously McCoy and his deputy Clingerman whose names often appeared together on docs from Sign).
Then AMC Project Sign regrouped to try again. The 2nd EOTS was drafted in late Sept 1948 after Craigie was replaced by Gen Don Putt as Dir of R&D at the Air Staff in the Pentagon on Sept. 1, 1948. Apparently AMC had the idea that this new Dir of R&D would be a second shot at gaining approval, as a kind of appeal from the previous decision. Apparently that didn't work but Putt authorized AMC to go over his head all the way up to Vandenberg if they liked (otherwise it would be violating the chain of command) however no one wanted to overturn Craigie on this appeal, so it was dead sometime in Oct 1948. This 2nd EOTS was the one Ruppelt described, thick and black-covered, apparently including a large volume of case reports (such as the Los Alamos sighting of Sept 23 which Ruppelt mentioned in the unpublished part of his manuscript was the last case included in this EOTS). Evidently AMC wanted a lot more documentation as backup on this 2nd attempt at the EOTS, which makes perfect sense.
This fits with what we know of a sudden disturbance in the Air Intelligence flying disc study ordered by Gen Cabell, AF Dir of Intelligence at the Pentagon, on July 27 and going on at the same time as Sign's study. On Aug 5-6, the AFOIN study was suddenly taken from the Air Estimates Branch which had been feverishly working on it for almost two weeks working toward a tight deadline for completion on Friday, Aug. 13, then extended to a Sunday (very unusual to have a Sunday deadline, indicates extreme urgency and high priority) Aug 15, 1948. The disc study was assigned to the more skeptical Defensive Air Branch which had the soon-to-become infamous debunker Maj Jeremiah Boggs on staff, and suddenly all the tight deadline crunches were relaxed.
My take on it is that when AMC's EOTS with its interplanetary conclusion was received at the Air Staff on Aug 5, 1948, pandemonium broke loose at AFOIN and the skeptics got the upper hand, seeing that (as I interpret events) Air Estimates was coming up with similar interplanetary conclusions (I can't prove they were similar, it's my inference since Estimates would historically be the home of the pro-UFO types including the later Dewey Fournet). So the high-level skeptical AFOIN officers (probably the nasty anti-UFO Chief of the Air Intelligence Division B/Gen Ernest "Dinty" Moore, who had both the AE and DA Branches under him) had the study transferred to a hostile group, at Defensive Air, and gave them plenty of time to do their business. No more Sunday deadlines, no more pressure, weeks went by, then months. A first draft was not done until October and then after it got upgraded to TOP SECRET, and after reviews and approvals it was issued on Dec. 5, 1948, for mainly internal AF and Navy dissemination, then reissued on April 28, 1949, for slightly broader interservice dissemination to Army, Navy, JCS and possibly some OSD agencies after discussion at the JCS Joint Intelligence Committee.