I haven't much to contribute on Rogue River, but will toss two cents in. This case occurs after SIGN has been whacked and the team has generally been dispersed to other duties. So, back at Grudge you have, basically Lt. H.W.Smith and civilian George Towles trying to go with the new flow and avoid trouble. The Sidney Shallet publication and the coincident "Project Saucer" release are out there doing their damages to information management control, and thus things aren't "comfortable" either at Wright-Pat or the Pentagon. This is mentioned to indicate that "prestige" UFO cases aren't welcome at the moment, and Towles and Smith have plenty of incentive to write them off. Howard McCoy was still nominally chief, but everyone knew that the winds had changed, and probably knew that Harold Watson was on his way. The latest "scary story" rumoring around both the military and the media [ex. NEPA and Walter Winchell] was that a Russian nuclear-powered saucer was possible. One wonders what the scuttlebutt on that was out at NACA on the West Coast.
At the end of April, Director of Intelligence, Charles Cabell, reported to the Joint Intelligence Committee [serving the Joint Chiefs of Staff] that "there are numerous reports from reliable and competent observers for which a conclusive explanation has not been made. Some of these involve descriptions which would place them in the category of new manifestations of probable natural phenomena, but others involve configurations and described performance which might conceivably represent an advanced aerodynamical development. A few unexplained incidents surpass these limits of credibility." I believe that you can hear in that last puzzling sentence an echo of the "Estimate". Regardless, one can see that a great deal of seriousness was still afoot at high levels even if Towles and Smith weren't aware of it. The May "Rogue River" Incident should be precisely the sort of thing that Cabell et al were concerned about. The witnesses were multiple and, apparently, outstanding---including a NACA wind tunnel employee and a NACA draftsman. The "thing" was viewed by eye and by binoculars, and seems to be a well detailed case with enough "strangeness" to easily qualify as an "unknown". Instead, on the project record card was typed [by Towles or Smith?]: "No data presented to indicate object could not have been an aircraft. Conclusion: aircraft." Well, the boys were just doing their job.