I was reading the British Chiefs of Staff Minutes and on 31 July 1945, they had fairly long discussions regarding ULTRA:
3. A great number of German official archives are now in the process of being sorted and translated and they will, in due course, be made available to the various official historical sections concerned. These archives will include references to the conduct of operations, the introduction and employment of new weapons and many other matters which have formed the subject of Special Intelligence during the war. It will be undesirable and indeed impossible to suppress the German records.
Reaction of Personnel of Historical Sections
4. When our official historians eventually study these German records they will analyse them in comparison with the relevant British documents with regard to operations and the employment of new weapons and techniques. It will then be revealed to them that the Naval, Army and Air staffs have, throughout the war, been in possession of information concerning energy movements and operational and technical intelligence which could not have been received from agents or other means slower than Special Intelligence. Obvious instances are the re-routeing of our convoys to avoid submarine attacks by orders issued immediately after the issue of German orders to their U-boats: the counter measures to meet the G.A.F. attacks on this country and the routeing of our deep penetration raids into Germany: the deployment of our forces in the field in face of German dispositions. On the technical side of intelligence the same insecurity will arise, upon analysis, when the date of the antidote to a new weapon is compared with the first known use of that weapon.
I suddenly then thought of the problem involving the CIS and the sudden end of the Clone Wars.
What happens to all the CIS data?
Surely the CIS high command must have been taking copious notes of when Darth Sidious was in contact with them and what he said to them?
I mean, if a mysterious stranger is talking to me over the holonet and causing me to instigate a galactic civil war, you bet your ass I'm gonna keep a burn file to protect my ass if it all goes pear shaped and I'm on trial for crimes against galactic peace.
That brings me to my point -- at the same time Anakin was executing Operation Knightsfall against the Jedi Temple; there must have been secret operations undertaken against the CIS leadership to destroy their data archives, so that the only source(s) left were the personal records of the CIS leadership, which they took with them to Mustafar, and were destroyed by Darth Vader after he executed the leadership.
Palpatine has the advantage in that he knows exactly when he talked to the CIS leadership or issued orders, so he can simply destroy all high level CIS records around those dates (plus random times to throw FUD into the mix). Also, he doesn't need to destroy 99.999% of all records involving him.
He just needs to destroy enough that even if some post-war Imperial Historian writing the history of the Clone Wars from captured CIS files sees a cryptic reference to "GALAHAD" (or whatever they called Sidious), there's enough data loss that the historian writes it off as "who the fuck knows what this is?"