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Stalin ordered some photographs to be altered because his enemies were in it. How did historians get their hands on the undoctored version? Because many a sources describe this as erasing the people from history by erasing them from the photographs. so how did they get their hand son the original?

I found the answer:

It’s thought that Stalin’s obsession with photo doctoring constituted a mini industry in the USSR. Publishers were contacted by Stalin’s minions and told to eliminate the enemy du jour from upcoming photos—and they did. According to art historian Peter King, who uncovered thousands of doctored photos and their original versions, the work was not performed in one location or even through an official ministry.

from How Photos Became a Weapon in Stalin’s Great Purge.

Originals of these doctored photographs of course survived. In most cases the photograph was published shortly after it was made. At a later time it was doctored and published again.
Then every effort was made to remove the original version from public circulation.
Let me mention that access to OLD newspapers was always restricted in Soviet times.
They were kept in some libraries in closed storages. To access this closed storage in scientific libraries for research purposes one had to obtain special permission.
Most public libraries did not keep old newspapers.

Moreover, books were removed from the libraries. My father was a director of a large scientific library in 1930s. He told me that EVERY WEEK special people came with the lists of books to be removed.

It was not illegal for a private person to collect books or newspapers. However, if some undesirable item was found in your possession, you would have to answer unpleasant questions, and most people tried to avoid this.

Anyway, all these old photographs could be eventually found in special storages and private collections.

Most of these doctored photographs included Lenin or Stalin with people who later became undesirable. After Stalin’s death this practice continued. For example when Beria was suddenly dismissed and killed, they had just printed the volume of Great Soviet Encyclopedia which contained a long article "Beria". All copies of this volume had to be urgently replaced. The new version had a VERY long
article about the Bering Strait, specially written to occupy the needed number of pages:-) Of course all photographs of Beria suddenly disappeared.
Same happened (on a smaller scale) with Khrushchev's portraits when he was dismissed.

Extraordinary efforts were made since June 1941 to remove all photographs of Molotov/Stalin together with Ribbentrop. But of course many survived as you can see on Internet. (And Ribbentrop paid with his life in the Nuremberg trial for these photographs).