There are a good number of national and regional statistics from 1943-44, statistics for the Reich persist for a while (despite the 'downsizing' of the Jewish councils), Theresienstadt is precisely documented and counted from start to finish.
The same applies for Poland, with a census in the Govt-General in March 1943, the tracking of numbers in the Warthegau and Lodz ghetto goes up to August 1944, and then one sees labour statistics in economics records. By mid-1944 the documentation shifts almost entirely to within the KZ system, since there were hardly any un-evacuated labour camps and after the Lodz action, no more ghettos in Poland.
The March 1943 GG census was down to 203,000 Jews, IIRC - figure is in Dieter Pohl's book on Ostgalizien and the Diensttagebuch. This from the stated 297,000 in the Korherr report, after actions resumed especially in Eastern Galicia. The transfers that followed meant a growing proportion were held in SS-run camps, which were extrajudicial spaces, so the census likely did not include Majdanek. By June 1943, Globocnik counted 45,000 Jews in forced labour camps in the Lublin district, this after the final liquidation of the Warsaw ghetto and transfer of the workshops to Poniatowa and Trawniki; and after the same set of camps were absorbing workers from the Bialystok district and Dutch transports. The number does not include Majdanek, but the bulge from May had been dispersed by then, some transports sent on to the Radom district camps. At the end of June 1943, there were only 21,000 Jews left alive in the forced labour camps of the Galicia district, and only a few thousand by the start of 1944 (mainly in Boryslaw and Drohobycz working in the oil fields).
I don't think there's a clear figure for the start of 1944 for Jews remaining in the GG, but the pattern with 1943 statistics is such that nobody can plausibly claim there were large numbers left by then.
Further east, and overlapping with prewar eastern Poland, the Reichskommissariat Ostland still imprisoned 72,000 Jews in July 1943, which breaks down well for the Riga ghetto, Lithuania and Minsk/Weissruthenien. The important thing here is to note that Himmler had ordered the transformation of the remaining ghettos to KZs, so by autumn 1943 one sees some liquidated (Minsk), some transferred (Wilno to KL Vaivara), and some converted locally, with various killing and deportation actions reducing the 72,000 number, e.g. children in the Lithuanian ghettos who had been tolerated as family members of work-certificate holders, are no longer tolerated.
The Reichskommissariat Ukraine was regarded as free of Jews with the exception of a small number of labour camps (on DG IV and one other, IIRC), which were liquidated before the Soviet reconquest. The Romanians resurveyed Transnistria several times so knew how many needed to be evacuated westwards before the Soviets overran it - part of Antonescu's reverse ferret on the 'Jewish question' once they started to look for ways of getting out of the war.
Survivors liberated in 1945 in Germany/Austria were composed of the survivors of several large groups transferred west in the summer of 1944: circa 110,000 Hungarian Jews selected for work at Auschwitz; 28,000 Lodz Jews selected at Auschwitz; several 10s of 1000s of Jews evacuated from the Baltic KZs via Stutthof; several 10s of 1000s evacuated from the force labour camps of the GG; the survivors in Auschwitz predating the Hungarian Action; some smaller numbers from the last transports from the rest of Europe; some thousands from the last wave of Theresienstadt transports and from Slovakia; and 10s of 1000s of Hungarian Jews force marched to Austria and absorbed either into Mauthausen or used in non-KZ forced labour camps in Austria.
Only the labour camp at Czestochowa and the clean-up crew in Lodz (878 survivors) were liberated inside Poland, followed by the 7000 (not all but mostly Jewish) prisoners liberated at Auschwitz on January 27, 1945. The Stutthof and Gross-Rosen complexes/main camps were evacuated fairly systematically at the same time as the Auschwitz evacuation.
