Max current capacity for 6ga is 125Amps, and the resistance is .01975ohms @50 ft. Max current capacity for #4 wire is 199 Amps and the resistance is .0124 @50 ft.
http://www.wiretron.com - pretty cool little calculator......
If you go from 12V to 48V - since the voltage is increased - the amperage is decreased (by the same factor of 4). So even if you increase the output of your generator by a factor of four (power) to 48V you won't see any increase in amps. If you are seeing 40 Amps at 12V and you switch that to 48V it would only be 10A (at the same power).
If I'm missing the gist of your question, let me know. There are many here that are more qualified to answer than I, so just use this as a guideline, the guru's can give you way more information than I can.
In general I would say that the higher the voltage you are able to go with, the smaller wire you are able to use, with less losses.
WP