Name your old bot "MyBot.cpp" and run "make.bat". Rename "MyBot" (application" and "MyBot.cpp" to "MyBotOld" and "MyBotOld.cpp". After that, make your new bot version "MyBot.cpp", then open "run_game.bat" and edit one of the "MyBot"'s to be "MyBotOld." Then just run "run_game.bat" and it should start a match between your two bots since the old one was already compiled.
Also, if you look up how to do loops in a batch file, you can separate "call make.bat" from the rest of the command and loop the game however many times you want. You only get 1 game of log files but you get n amount of replays.