Circumstances varied considerably, but the burial of casualties during the war was generally the responsibility of the military or civilian authorities of the area where they landed. Early in the war or in isolated areas aircrew might be buried in a local cemetery; for example casualties from Bomber Command's first raid of the war on German ships at Wilhelmshaven were taken to Geestemünde Cemetery in Bremerhaven.

The 1929 Geneva Convention for the Amelioration of the Condition of the Wounded and Sick in Armies in the Field stated: "Belligerents shall communicate to each other reciprocally, as soon as possible, the names of the wounded, sick and dead, collected or discovered, together with any indications which may assist in their identification. They shall establish and transmit to each other the certificates of death. They shall likewise collect and transmit to each other all articles of a personal nature found on the field of battle or on the dead, especially one half of their identity discs, the other hall to remain attached to the body. They shall ensure that the burial or cremation of the dead is preceded by a careful, and if possible medical, examination of the bodies, with a view to confirming death, establishing identity and enabling a report to be made. They shall further ensure that the dead are honourably interred, that their graves are respected and marked so that they may always be found. To this end, at the commencement of hostilities, they shall organize officially a graves registration service, to render eventual exhumations possible, and to ensure the identification of bodies whatever may be the subsequent site of the grave. After the cessation of hostilities they shall exchange the list of graves and of dead interred in their cemeteries and elsewhere."

Germany (broadly) adhered to the Geneva Conventions (with respect to the Western Allies), and supplied Death Lists (Totenlisten) to the International Committee of the Red Cross (ICRC), who in turn passed the information on to the British. Bodies could not always be clearly identified, particularly from violent crashes, and the British fibre identity discs could degrade. Other complications included at least one instance of a WAAF appearing on a Totenlist after she swapped ID discs with her boyfriend who was subsequently shot down.

As the war progressed and the scale of bombing dramatically increased larger concentration cemeteries were established, particularly in heavily bombed areas such as the Ruhr. Towards the end of the war less care was taken over burials, crew being left near their aircraft or even thrown into bomb craters in some cases. Record keeping was perfunctory, the loss of records in air raids being a further complication.

The Air Ministry established a Casualty Branch (P4(cas)) who gathered information on missing aircrew, liaised with relatives, and performed investigations via the Missing Research and Enquiry Service (MRES). As the war progressed and the Allies advanced into Europe, so the MRES advanced with them; indeed their efforts increased in scale after Germany surrendered with a number of Missing Research and Enquiry Units (MREUs) operating across the continent into 1949 (though it became increasingly difficult in Soviet-occupied areas as relations deteriorated). The MREUs investigated both reported and previously unknown crash sites, going to considerable lengths to attempt to trace the 41,881 missing RAF personnel across the world at the end of war - there was even an instance, in 1948, of a search officer taking a gravedigger to a psychiatrist for hypnosis to help him remember exactly where he had buried the crew of a Mosquito.

The question of the final resting place for war dead went to the Cabinet; firstly there was the issue of repatriation, and it was decided to continue the First World War policy that there would be no repatriation from overseas (in contrast with the US, who would repatriate the majority of their casualties). Then there was the issue over whether graves should be left in Germany; "There is undoubtedly a body of opinion in this country which would be against leaving the bodies of our men in German soil" as a report at the time noted. Noting the complexity of mass removal, though, the report recommended the concentration of graves in British Military Cemeteries under the Imperial (now Commonwealth) War Graves Commission, this policy being adopted by the government.

Your great uncle may well, then, have been located by an MREU before being relocated to the Berlin cemetery by the Army Graves Service.

Jennie Mack Gray's 2016 thesis ‘NOTHING CAN EXCUSE US IF WE FAIL’: The British and their Dead Servicemen, North-West Europe, 1944-1951 is superb on the subject; Mary Hudson's RAF WWII Operational and Flying Accident Casualty Files in the National Archives is also very good on the procedures adopted around the world.