I'd like to learn more about your workflow. Would it be possible to include screenshots?
The layer that you are using as your source layer must have the correct classification method. You are not able to change classification methods using arcpy.mapping. Reclassify essentially refreshes the layer against the source data (this is especially useful when using UpdateLayer). If your classification methods are different I would expect things to get "clobbered". You can always programatically control the breaks, labels, etc using arcpy.mapping.
Again, it would be nice to see more of what you are trying to do.
Jeff