It should now be obvious that during the two centuries of smallpox vaccination and up until the 1990s there was no certain way of testing for distinct orthopox viruses. During the two centuries of vaccination, the viruses were likely to mutate, and certain strains could have been selected out as a result of vaccination.
Therefore, does anyone know how much ‘smallpox’ disease was actually monkeypox or vaccinia? Given that monkeypox is thought to be an ancient virus, where was it during the smallpox epidemics? Was it called hemorrhagic smallpox?
In 1972, scientists were asking similar questions when they said:
“Is it possible that there is an animal reservoir for smallpox infection? Could monkeypox be a source of new outbreaks of true variola? Or, can the monkeypox virus undergo certain mutations and become identical in its pathogenicity and infectiveness to the variola virus?” 
ACCORDING TO SCIENTIFIC AMERICAN, monkeypox is not that rare. Seven hundred and sixty cases of monkeypox were counted in the Congo between 2006 and 2007.
Before and during the time of eradication declaration, PCR was unavailable, and the different poxviruses couldn’t be distinguished by their DNA, but by a skin test on rabbits, chick embryo membranes, and blood tests that were fraught with uncertainty. It seems to me that what was once called smallpox was likely a very non-uniform disease that could have been anything from cowpox to two forms of smallpox to chickenpox to monkeypox.
“Monkeypox virus is closely related to some other orthopoxviruses such as variola (smallpox) virus, and it cannot be distinguished from these viruses in some laboratory tests….In 1996-1997, an outbreak [of monkeypox] in the DRC continued for more than a year, with a person–to–person transmission rate estimated at 78%. However, epidemiological evidence suggests that many of the cases in this outbreak may have been chickenpox (varicella); the number of monkeypox cases and the transmission rate might have been overestimated due to self-reporting and the unavailability of laboratory testing.” 
When vaccination stopped, monkeypox was suddenly diagnosed in humans. Diagnostic methods were absent during the great vaccine campaigns and everything pox-like was considered smallpox and counted as smallpox. Differentiating was not a priority.
Variola, the smallpox virus, is not in the smallpox vaccine. Instead, a cultured form of cowpox, called vaccinia, is the virus used to prevent smallpox. That same vaccine also covers monkeypox, according to the CDC:
Smallpox vaccine is effective at protecting people against monkeypox when it is given before they are exposed to monkeypox. (Exposure includes very close contact with a person or animal that has monkeypox.) Experts believe that vaccination after exposure to monkeypox may help prevent the disease or make it less severe.“ 
"Because the monkeypox virus is related to the virus that causes smallpox, the smallpox vaccine can protect people from getting monkeypox as well as smallpox.
Even though PCR can distinguish between the three viruses, clinically and immunologically the viruses are so similar, that one virus in the vaccine is thought to immunize against the two other viruses. During outbreaks they all look the same.