Lets not confuse show channels with controller channels. While the show channels run up sequentially from 1 to whatever, the controller channels are ALWAYS from 1 up to the universe limit. In DMX, that would be 512 and in PixelNet, that would be 4096. Also keep in mind that there are NO channel numbers in the data stream. They are positional so the first one in the stream is channel one and the 5th is channel 5 and the 120th is channel 120 and on it goes either up to the universe limit or the next start of string indicator is read. When you set the start channel of the controller, it counts the data bytes or channels from the beginning of string indicator until it gets to the start channel assigned to it and then begins loading them up to either its limit or the end of the stream, whichever comes first. This is why your setting the start channel to 4097 didn't work, because there is no 4097th or higher channel in the stream, it only has 4096 and when it gets to 4096, instead of seeing 4097, it sees a beginning of string indicator and resets and begins counting again, never loading any data.
This is why we have multiple universes. The trick to it is to properly configure the show software to send the required channels to the proper output universes. In your example, you would send the first 4096 channels to USB dongle one and the rest to the second USB dongle and that is done in the output controllers definition. In your case, if you are using a combiner, I would plug the first dongle assigned to the first 4096 channels into the universe 1 port and the second into the universe 2 port. Then you can set your Zeus to use universe 2 and it will get its data from the second dongle but remember, it is still working from controller channel 1 because regardless of how you defined the outputs, the first show channel number sent to the dongle is always seen as channel one to it and will be channel 1 in the output data stream. If you defined the first dongle for 4096 channels and the rest to dongle 2, then show channel 1 is channel 1 on universe 1 and show channel 4097 will be channel 1 on universe 2.