No, downloading or uploading maps into the PC does not affect the stage flash in the ECM.
Depending on wether you have the stock ECM flash or the stage 1 flash you would need a different map for the PC. In addition you would need complete and exact information on everything that has been put on the bike, to even begin to take a guess at a map.
On a 02 bike you only need either one, stage flash or PC, or both if you wish, if you go beyond reasonable pipes.
I'm not sure that a PC is a good idea unless absolutely necessary, when there is no local tech support. PC's are great when you know what you are doing, but can very easily screw things up if not programmed right for the bike, and even a good map has to be tweaked more often then not.
There is no one in Mexico City at this time that can build a map off the bike, as far as I know.