"A quite well informed participant of the top level negotiations among the Allies reports:
Ever since (his) visit to Moscow in the winter (of 1941/42), ... Eden ...argued that the recognition of the boundaries Stalin claimed was a small price to pay for Soviet cooperation in the war, even if this meant that the peoples of Estonia, Latvia and Lithuania were forever consigned to Russian overlordship.
The British were determined to conclude as soon as possible an Anglo-Soviet treaty of alliance, whatever the price. The secret correspondence between Churchill and Roosevelt is very informative. It includes a letter of March 7, 1942, in which Churchill writes:"(British Ambassador to the U.S.) Halifax reported, "Mr. Eden cannot incur the danger of antagonizing Stalin, and
the British War Cabinet have ...agree(d) to negotiate a treaty with Stalin, which will recognize the 1940 frontiers of the Soviet Union..." 
[I] feel that the principle of the Atlantic Charter ought not to be constructed so as to deny Russia the frontiers she occupied when Germany attacked her. This was the basis on which Russia accepted the Charter, and I expect that a severe process of liquidating hostile elements in the Baltic States, etc., was employed by the Russians when they took these regions at the beginning of the war. I hope, therefore, that you will be able to give us a free hand to sign the treaty, which Stalin desires as soon as possible.
The consent was evidently given, and the treaty was signed on May 26, 1942. Roosevelt seems to have accepted the argument that it would not be fair to deny the Baltic countries to the Russians, who had worked so hard "severely eliminating hostile elements" there...
What about the solemn promises in the Atlantic Charter? It seems to have been mere wartime propaganda ploy to be applied or disregarded at will. It was not applied either to the British or the Soviet empire. Churchill confirms that in a secret letter to Roosevelt on Feb. 2, 1943:
Russia has signed a treaty with Great Britain on the basis of Atlantic Charter binding both nations mutually to aid each other....By it and by Atlantic Charter the two nations renounce all idea of territorial gains. Russians no doubt (! - V.V.Š.) interpret this as giving them right to claim ...their frontier of June 1941...Churchill also agreed with Stalin to divide their spheres of influence in Eastern Europe when they met in Moscow, October 9, 1944. In the words of the British Prime Minister himself:
The moment was apt for business, so I said, "Let us settle about our affairs in the Balkans. - - - Russia ...(is) to have ninety per cent predominance in Rumania, for us to have ninety per cent of the say in Greece, and to go fifty-fifty about Yugoslavia....
Churchill then added a 50-50 split for Hungary and gave Stalin a 75-25 predominance in Bulgaria.
It was all settled in no more time than it takes to set down. ... The pencilled paper lay in the center of the table. At length I said, "Might it not be thought rather cynical if it seemed that we had disposed of these issues, so fateful to millions of people, in such an offhand manner? Let us burn the paper." — "No, you keep it," said Stalin.""