This should be possible if you are using the instance API that AutoMapper provides instead of the static API. This wiki page details the differences between the two.
Essentially, instead of calling AutoMapper.Mapper.Initialize(cfg => ...) again for your additional mapping, which overwrites the entire global mapping configuration with this single mapping, you need to create another mapper object with the instance API using:
var config = new MapperConfiguration(cfg => cfg.CreateMap<CustomerModel, CustomerInfoModel>() ); var mapper = config.CreateMapper();
Of course, to use this new cartographer, you will need to do something like var mappedModel = mapper.Map<CustomerInfoModel>(new CustomerModel()); specifically when matching objects using your optional matching configuration. How practical this is in your case, I do not know, but I believe that this is the only way to do what you need.
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